This document analyzes data from an Ion Torrent 400bp chip sequencing run of the Sedum album genome. It finds that the original 400bp reads have high error rates, with 25% insertions, 33% deletions, and 85% mismatches when mapped. However, error correction reduces these rates to 10% insertions, 15% deletions, and 70% mismatches. Both the original and corrected reads show decreasing base quality after 100bp and an overrepresentation of k-mers from 150-450bp. The analysis provides detailed mapping and alignment statistics comparing the original and corrected reads.
The document summarizes Ion Torrent next generation sequencing. It detects chemiluminescence given off when a proton is released during sequencing. DNA fragments are attached to beads and undergo emulsion PCR amplification. Sequencing is based on standard pyrosequencing and measures light from chemiluminescent reagents released during the reaction. The output is in FASTQ format.
Ion torrent semiconductor sequencing technologyCD Genomics
Ion Torrent is the latest generation sequencing technology. Its core technology is the use of semiconductor technology in chemical and digital information to establish a direct link.
Powered by Ion Torrent™ semiconductor chip technology, the Ion Proton™ Sequencer is the first benchtop next-generation sequencer to offer fast, affordable human genome and human exome sequencing. Powered by the next generation of semiconductor sequencing technology and offering a similar single-day workflow to the Ion PGM™ Sequencer, the Ion Proton™ Sequencer promises to change the way scientists look at genomics.
For more information visit:
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Sequencing/Semiconductor-Sequencing/proton.html?CID=Protonbrochure-SS-12312
This document provides a flow diagram for genome assembly. It outlines several key steps: linking read files and removing redundant and low quality reads; trimming adaptors and filtering contamination; analyzing GC content and k-mers to estimate genome size; joining reads to span gaps; and assembling fragments into the original sequence using de novo assembly software. The overall goal is to preprocess and assemble genomic reads into a reconstructed genome sequence.
This document discusses the potential for metagenomics to provide novel enzymes and biocatalysts for various industrial applications. It outlines how different industries, such as chemicals, pharmaceuticals, and detergents, are interested in accessing new enzymes from uncultured microbes. The document also discusses challenges in finding suitable enzymes and describes screening methods used to identify candidate enzymes from metagenomic libraries for specific industrial transformations and processes.
The document discusses how epigenetics, through mechanisms like DNA methylation and histone modification, can influence gene expression and traits without changing the underlying DNA sequence. It provides examples of how environmental factors and early life experiences can alter the epigenome in ways that affect health conditions later in life, including cancer, mental illnesses like schizophrenia, and neurodevelopmental disorders. Epigenetic therapies targeting these epigenetic changes offer promising new medical approaches.
This document discusses structural genomics and its goals of determining the 3D structures of large numbers of gene products to identify novel protein folds and sequences. It describes methods for structural determination including de novo and modeling based approaches. Specific proteome projects on Thermotoga maritima and Mycobacterium tuberculosis are mentioned. The objectives of structural genomics are outlined as providing structural information to aid research, experimental design, identification of new structure-based medicines, and development of better therapeutics.
Structural genomics aims to determine the 3D structure of all proteins in a genome. It uses high-throughput methods like X-ray crystallography and NMR on a genomic scale. This allows determination of protein structures for entire proteomes. It provides insights into protein function and can aid drug discovery by identifying potential drug targets like in Mycobacterium tuberculosis. Structural genomics leverages completed genome sequences to clone and express all encoded proteins for structural characterization.
The document summarizes Ion Torrent next generation sequencing. It detects chemiluminescence given off when a proton is released during sequencing. DNA fragments are attached to beads and undergo emulsion PCR amplification. Sequencing is based on standard pyrosequencing and measures light from chemiluminescent reagents released during the reaction. The output is in FASTQ format.
Ion torrent semiconductor sequencing technologyCD Genomics
Ion Torrent is the latest generation sequencing technology. Its core technology is the use of semiconductor technology in chemical and digital information to establish a direct link.
Powered by Ion Torrent™ semiconductor chip technology, the Ion Proton™ Sequencer is the first benchtop next-generation sequencer to offer fast, affordable human genome and human exome sequencing. Powered by the next generation of semiconductor sequencing technology and offering a similar single-day workflow to the Ion PGM™ Sequencer, the Ion Proton™ Sequencer promises to change the way scientists look at genomics.
For more information visit:
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Sequencing/Semiconductor-Sequencing/proton.html?CID=Protonbrochure-SS-12312
This document provides a flow diagram for genome assembly. It outlines several key steps: linking read files and removing redundant and low quality reads; trimming adaptors and filtering contamination; analyzing GC content and k-mers to estimate genome size; joining reads to span gaps; and assembling fragments into the original sequence using de novo assembly software. The overall goal is to preprocess and assemble genomic reads into a reconstructed genome sequence.
This document discusses the potential for metagenomics to provide novel enzymes and biocatalysts for various industrial applications. It outlines how different industries, such as chemicals, pharmaceuticals, and detergents, are interested in accessing new enzymes from uncultured microbes. The document also discusses challenges in finding suitable enzymes and describes screening methods used to identify candidate enzymes from metagenomic libraries for specific industrial transformations and processes.
The document discusses how epigenetics, through mechanisms like DNA methylation and histone modification, can influence gene expression and traits without changing the underlying DNA sequence. It provides examples of how environmental factors and early life experiences can alter the epigenome in ways that affect health conditions later in life, including cancer, mental illnesses like schizophrenia, and neurodevelopmental disorders. Epigenetic therapies targeting these epigenetic changes offer promising new medical approaches.
This document discusses structural genomics and its goals of determining the 3D structures of large numbers of gene products to identify novel protein folds and sequences. It describes methods for structural determination including de novo and modeling based approaches. Specific proteome projects on Thermotoga maritima and Mycobacterium tuberculosis are mentioned. The objectives of structural genomics are outlined as providing structural information to aid research, experimental design, identification of new structure-based medicines, and development of better therapeutics.
Structural genomics aims to determine the 3D structure of all proteins in a genome. It uses high-throughput methods like X-ray crystallography and NMR on a genomic scale. This allows determination of protein structures for entire proteomes. It provides insights into protein function and can aid drug discovery by identifying potential drug targets like in Mycobacterium tuberculosis. Structural genomics leverages completed genome sequences to clone and express all encoded proteins for structural characterization.
Geiger–Müller Counter is a hand-held radiation survey instrument used in Radiation Dosimetry,Nuclear Physics,Experimental Physics & Radiological Protection.
A Geiger-Muller counter consists of a gas-filled tube that detects ionizing radiation such as alpha particles, beta particles, and gamma rays. When radiation enters the tube, it ionizes the gas and produces a pulse of current that is counted by a scaler. To prevent additional pulses from a single radiation event, a small amount of quenching gas is added which absorbs excess energy and prevents further ionization of the main gas. The Geiger-Muller counter has a dead time after each detection where it cannot detect additional radiation as it re-establishes the electric field inside the tube.
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
New Generation Sequencing Technologies: an overviewPaolo Dametto
The document provides a history of DNA sequencing technologies. It begins with the discovery of DNA's structure in 1953 and the development of recombinant DNA technology in the 1970s. First generation Sanger sequencing produced short reads over 1,000 years to sequence the human genome. Next generation sequencing (NGS) platforms since 2005 have dramatically reduced costs while increasing throughput. NGS methods like Roche/454 pyrosequencing, Illumina/Solexa sequencing by synthesis, SOLiD ligation sequencing, and single-molecule real-time sequencing by Pacific Biosciences now enable large-scale genome and transcriptome analysis.
The document summarizes the Geiger-Müller counter, an instrument used to detect ionizing radiation such as alpha particles, beta particles, and gamma rays. It describes the history and development of the counter, from its original detection principle discovered in 1908 to its modern form using a Geiger-Müller tube. The operating principle is explained, where ionization events in an inert gas-filled tube produce electrical pulses that are counted and displayed. Different readout types including counts per second and absorbed dose are discussed. Applications include detection of radioactive materials and environmental monitoring for radiation levels.
This document discusses metagenomics, which is the study of microbial communities directly in their natural environments without isolating individual species. It outlines some key aspects of metagenomics including that most prokaryotes cannot be cultured, the use of metagenomics to study viral communities, and approaches such as functional screening and sequence-based screening. Limitations and future directions are also mentioned. Metagenomics provides insights into microbial interactions, metabolism, and genomics that were previously unknown.
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
NGS technologies - platforms and applicationsAGRF_Ltd
This document summarizes several next-generation sequencing platforms and applications. It describes the workflows and chemistries of 454, Illumina, SOLiD, and Ion Torrent platforms. These platforms have significantly reduced the cost of sequencing compared to Sanger sequencing. Common applications include whole genome sequencing, RNA sequencing, sequence capture, and amplicon sequencing. Library preparation requires fragmentation of DNA or RNA, addition of adapters, and amplification prior to sequencing.
This document provides an overview and comparison of popular next-generation sequencing platforms. It discusses the common sequencing pipeline including library preparation, massively parallel sequencing, and bioinformatics analysis. Popular platforms like Roche 454, Illumina, and SOLiD are described in detail focusing on their specific sequencing chemistries and performance characteristics. Newer third-generation platforms such as Ion Torrent, PacBio, and Oxford Nanopore are also introduced. A wide range of NGS applications from whole genome sequencing to RNA-seq are outlined.
This document provides an introduction to next generation sequencing (NGS) technologies. It begins with an outline of topics to be covered, including the evolution of NGS technologies, their descriptions and comparisons, bioinformatics challenges of NGS data analysis, and some aspects of NGS data analysis workflows and tools. The document then delves into explanations of specific NGS platforms, their performance characteristics, and the sequencing processes. It discusses the large computational infrastructure and data management needs of NGS, as well as quality control, preprocessing of NGS data, and popular analysis tools and workflows.
GaN-on-Silicon Transistor Comparison 2018 Structural, Process & Costing Repor...Yole Developpement
Dive deep into the technology and cost of GaN-on-silicon HEMTs from EPC, Transphorm, GaN Systems, Panasonic and Texas Instruments.
More information on that report at https://www.i-micronews.com/report/product/gan-on-silicon-transistor-comparison-2018.html
Deep dive analysis of the fourth generation of mid/high band front-end module for 4G and 5G from Broadcom.
More information : https://www.systemplus.fr/reverse-costing-reports/broadcom-afem-8200-pamid-in-the-apple-iphone-12-series/
Solution on Portable Blood Pressure Monitor SystemPremier Farnell
The document discusses the design of a portable blood pressure monitor system using a Freescale MCF51QE128 microcontroller. It outlines the system architecture including components like a pressure sensor, LCD display, and battery management. Evaluation boards, peripherals, and additional resources for designing such a system are also presented.
Broadcom AFEM-8072 – Mid and High Band LTE RF Front-End Module (FEM) - teardo...system_plus
The first mid/high band Long Term Evolution (LTE) Radio Frequency (RF) FEM in the Apple iPhone X integrates the latest generation of Film Bulk Acoustic Resonator (FBAR) technology with advanced and innovative packaging.
More information on that report at http://www.systemplus.fr/reverse-costing-reports/broadcom-afem-8072-mid-and-high-band-lte-rf-front-end-module-fem/
Broadcom AFEM-8100 System-in-Package in the Apple iPhone 11 Seriessystem_plus
This document provides a reverse costing analysis of the Broadcom AFEM-8100 SiP used in the Apple iPhone 11 series. It includes a physical analysis of the module and its dies, as well as a manufacturing process flow and cost analysis. Broadcom remains the sole supplier of the multi-die module, which features power amplifier, switch, filter and other dies. The analysis finds innovations that reduce the package size and cost, including a new EMI shielding integration method.
PAM4 Analysis and Measurement Considerations WebinarHilary Lustig
This webinar explores the acquisition and analysis of PAM4 waveforms. We will show PAM4 Test Configurations, Compliance Measurements and Debug Techniques.
PAM4 Analysis and Measurement Webinar Slidedeckteledynelecroy
In this Teledyne LeCroy webinar we explore the acquisition and analysis of PAM4 waveforms. We will cover PAM4 test configurations, compliance measurements and debug techniques.
BEST PRACTICE TO MAXIMIZE THROUGHPUT WITH NANOPORE TECHNOLOGY & DE NOVO SEQUE...Baptiste Mayjonade
1) The document discusses best practices for maximizing throughput when using Nanopore technology, including ensuring high purity and integrity of input DNA samples.
2) It describes using Nanopore sequencing to generate de novo reference genomes for genetic lines of Arabidopsis thaliana, with high quality assemblies obtained.
3) Generating long reads with Nanopore allows detection of structural variations between genomes, with the potential to improve genome-wide association mapping.
Abdul Mozid: New developments in wire based antegrade approachEuro CTO Club
14th Experts "Live" CTO
September 2nd- 3rd, 2022 - Mainz, Germany
Main Session - Session 2:
Selecting the patient and planning the procedure B
New developments in wire based antegrade approach
Abdul Mozid, Leeds, United Kingdom
Room:
Guteberg Hall (Auditorium) - Friday 13:20
Chairmen:
Alexander Bufe, Krefeld, Germany;
Leszek Bryniarski, Krakow, Poland;
Hans Bonnier, Nuenen, Belgium
2-Axis Gyroscopes for Optical Image Stabilization: STMicroelectronics L2G2IS ...Yole Developpement
Complete reports and comparison of the latest generation products for smartphones from the leading optical image stabilization gyro players.
2-Axis Gyroscopes for Optical Image Stabilization (OIS) constitute a market where 123 million units were shipped in 2015, according to Yole Développement. This market originates only from high-end smartphones and two players share most of it: InvenSense, with 49%, and STMicroelectronics, with 39%.
The 2-axis gyroscopes are located inside the camera module of high-end smartphones. The main constraints are a small footprint and, more importantly, thinness.
Previously, thickness was the same as standard land grid array (LGA) or quad flat no-leads (QFN) package, close to 1mm. Now the standard is 0.65mm, which products from both InvenSense and STMicroelectronics attain.
InvenSense was first, with the IDG-2030, a 2.3x2.3x0.65mm gyroscope, which is still the smallest on the market. Since its introduction we found it in several smartphones from various manufacturers. The IDG-2030 uses the same Nasiri platform as other InvenSense inertial devices, with wafer-level integration of the MEMS sensor on top of the application specific integrated circuit (ASIC), thus providing only one die in the final LGA package.
Months later, STMicroelectronics released the L2G2IS, which shares the same dimensions. The device is manufactured using the same THELMA process as all STMicroelectronics inertial devices. The THELMA platform involves a two-die approach that is challenging for very thin package integration. However, both players now offer very low-cost gyros thanks to die size reduction and process optimization.
Both gyroscopes analyzed are 2-axis X, Y (Pitch, Roll). The two reports can be purchased separately or together in order to compare the technology and pricing of the main smartphone OIS gyro players, including previous generation products.
More information on that report at http://www.i-micronews.com/reports.html
Geiger–Müller Counter is a hand-held radiation survey instrument used in Radiation Dosimetry,Nuclear Physics,Experimental Physics & Radiological Protection.
A Geiger-Muller counter consists of a gas-filled tube that detects ionizing radiation such as alpha particles, beta particles, and gamma rays. When radiation enters the tube, it ionizes the gas and produces a pulse of current that is counted by a scaler. To prevent additional pulses from a single radiation event, a small amount of quenching gas is added which absorbs excess energy and prevents further ionization of the main gas. The Geiger-Muller counter has a dead time after each detection where it cannot detect additional radiation as it re-establishes the electric field inside the tube.
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
New Generation Sequencing Technologies: an overviewPaolo Dametto
The document provides a history of DNA sequencing technologies. It begins with the discovery of DNA's structure in 1953 and the development of recombinant DNA technology in the 1970s. First generation Sanger sequencing produced short reads over 1,000 years to sequence the human genome. Next generation sequencing (NGS) platforms since 2005 have dramatically reduced costs while increasing throughput. NGS methods like Roche/454 pyrosequencing, Illumina/Solexa sequencing by synthesis, SOLiD ligation sequencing, and single-molecule real-time sequencing by Pacific Biosciences now enable large-scale genome and transcriptome analysis.
The document summarizes the Geiger-Müller counter, an instrument used to detect ionizing radiation such as alpha particles, beta particles, and gamma rays. It describes the history and development of the counter, from its original detection principle discovered in 1908 to its modern form using a Geiger-Müller tube. The operating principle is explained, where ionization events in an inert gas-filled tube produce electrical pulses that are counted and displayed. Different readout types including counts per second and absorbed dose are discussed. Applications include detection of radioactive materials and environmental monitoring for radiation levels.
This document discusses metagenomics, which is the study of microbial communities directly in their natural environments without isolating individual species. It outlines some key aspects of metagenomics including that most prokaryotes cannot be cultured, the use of metagenomics to study viral communities, and approaches such as functional screening and sequence-based screening. Limitations and future directions are also mentioned. Metagenomics provides insights into microbial interactions, metabolism, and genomics that were previously unknown.
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
NGS technologies - platforms and applicationsAGRF_Ltd
This document summarizes several next-generation sequencing platforms and applications. It describes the workflows and chemistries of 454, Illumina, SOLiD, and Ion Torrent platforms. These platforms have significantly reduced the cost of sequencing compared to Sanger sequencing. Common applications include whole genome sequencing, RNA sequencing, sequence capture, and amplicon sequencing. Library preparation requires fragmentation of DNA or RNA, addition of adapters, and amplification prior to sequencing.
This document provides an overview and comparison of popular next-generation sequencing platforms. It discusses the common sequencing pipeline including library preparation, massively parallel sequencing, and bioinformatics analysis. Popular platforms like Roche 454, Illumina, and SOLiD are described in detail focusing on their specific sequencing chemistries and performance characteristics. Newer third-generation platforms such as Ion Torrent, PacBio, and Oxford Nanopore are also introduced. A wide range of NGS applications from whole genome sequencing to RNA-seq are outlined.
This document provides an introduction to next generation sequencing (NGS) technologies. It begins with an outline of topics to be covered, including the evolution of NGS technologies, their descriptions and comparisons, bioinformatics challenges of NGS data analysis, and some aspects of NGS data analysis workflows and tools. The document then delves into explanations of specific NGS platforms, their performance characteristics, and the sequencing processes. It discusses the large computational infrastructure and data management needs of NGS, as well as quality control, preprocessing of NGS data, and popular analysis tools and workflows.
GaN-on-Silicon Transistor Comparison 2018 Structural, Process & Costing Repor...Yole Developpement
Dive deep into the technology and cost of GaN-on-silicon HEMTs from EPC, Transphorm, GaN Systems, Panasonic and Texas Instruments.
More information on that report at https://www.i-micronews.com/report/product/gan-on-silicon-transistor-comparison-2018.html
Deep dive analysis of the fourth generation of mid/high band front-end module for 4G and 5G from Broadcom.
More information : https://www.systemplus.fr/reverse-costing-reports/broadcom-afem-8200-pamid-in-the-apple-iphone-12-series/
Solution on Portable Blood Pressure Monitor SystemPremier Farnell
The document discusses the design of a portable blood pressure monitor system using a Freescale MCF51QE128 microcontroller. It outlines the system architecture including components like a pressure sensor, LCD display, and battery management. Evaluation boards, peripherals, and additional resources for designing such a system are also presented.
Broadcom AFEM-8072 – Mid and High Band LTE RF Front-End Module (FEM) - teardo...system_plus
The first mid/high band Long Term Evolution (LTE) Radio Frequency (RF) FEM in the Apple iPhone X integrates the latest generation of Film Bulk Acoustic Resonator (FBAR) technology with advanced and innovative packaging.
More information on that report at http://www.systemplus.fr/reverse-costing-reports/broadcom-afem-8072-mid-and-high-band-lte-rf-front-end-module-fem/
Broadcom AFEM-8100 System-in-Package in the Apple iPhone 11 Seriessystem_plus
This document provides a reverse costing analysis of the Broadcom AFEM-8100 SiP used in the Apple iPhone 11 series. It includes a physical analysis of the module and its dies, as well as a manufacturing process flow and cost analysis. Broadcom remains the sole supplier of the multi-die module, which features power amplifier, switch, filter and other dies. The analysis finds innovations that reduce the package size and cost, including a new EMI shielding integration method.
PAM4 Analysis and Measurement Considerations WebinarHilary Lustig
This webinar explores the acquisition and analysis of PAM4 waveforms. We will show PAM4 Test Configurations, Compliance Measurements and Debug Techniques.
PAM4 Analysis and Measurement Webinar Slidedeckteledynelecroy
In this Teledyne LeCroy webinar we explore the acquisition and analysis of PAM4 waveforms. We will cover PAM4 test configurations, compliance measurements and debug techniques.
BEST PRACTICE TO MAXIMIZE THROUGHPUT WITH NANOPORE TECHNOLOGY & DE NOVO SEQUE...Baptiste Mayjonade
1) The document discusses best practices for maximizing throughput when using Nanopore technology, including ensuring high purity and integrity of input DNA samples.
2) It describes using Nanopore sequencing to generate de novo reference genomes for genetic lines of Arabidopsis thaliana, with high quality assemblies obtained.
3) Generating long reads with Nanopore allows detection of structural variations between genomes, with the potential to improve genome-wide association mapping.
Abdul Mozid: New developments in wire based antegrade approachEuro CTO Club
14th Experts "Live" CTO
September 2nd- 3rd, 2022 - Mainz, Germany
Main Session - Session 2:
Selecting the patient and planning the procedure B
New developments in wire based antegrade approach
Abdul Mozid, Leeds, United Kingdom
Room:
Guteberg Hall (Auditorium) - Friday 13:20
Chairmen:
Alexander Bufe, Krefeld, Germany;
Leszek Bryniarski, Krakow, Poland;
Hans Bonnier, Nuenen, Belgium
2-Axis Gyroscopes for Optical Image Stabilization: STMicroelectronics L2G2IS ...Yole Developpement
Complete reports and comparison of the latest generation products for smartphones from the leading optical image stabilization gyro players.
2-Axis Gyroscopes for Optical Image Stabilization (OIS) constitute a market where 123 million units were shipped in 2015, according to Yole Développement. This market originates only from high-end smartphones and two players share most of it: InvenSense, with 49%, and STMicroelectronics, with 39%.
The 2-axis gyroscopes are located inside the camera module of high-end smartphones. The main constraints are a small footprint and, more importantly, thinness.
Previously, thickness was the same as standard land grid array (LGA) or quad flat no-leads (QFN) package, close to 1mm. Now the standard is 0.65mm, which products from both InvenSense and STMicroelectronics attain.
InvenSense was first, with the IDG-2030, a 2.3x2.3x0.65mm gyroscope, which is still the smallest on the market. Since its introduction we found it in several smartphones from various manufacturers. The IDG-2030 uses the same Nasiri platform as other InvenSense inertial devices, with wafer-level integration of the MEMS sensor on top of the application specific integrated circuit (ASIC), thus providing only one die in the final LGA package.
Months later, STMicroelectronics released the L2G2IS, which shares the same dimensions. The device is manufactured using the same THELMA process as all STMicroelectronics inertial devices. The THELMA platform involves a two-die approach that is challenging for very thin package integration. However, both players now offer very low-cost gyros thanks to die size reduction and process optimization.
Both gyroscopes analyzed are 2-axis X, Y (Pitch, Roll). The two reports can be purchased separately or together in order to compare the technology and pricing of the main smartphone OIS gyro players, including previous generation products.
More information on that report at http://www.i-micronews.com/reports.html
The world’s smallest MEMS barometer for smartphone and smartwatch, with a lot of innovation
The LPS22HB Nano Pressure Sensor is the world’s smallest barometric sensor, incorporating the VENSENS process and the new BASTILLE process, featuring abundant design innovation. Targeting altitude and weather forecasting applications in portable devices, this MEMS sensor positions STMicroelectronics for double-digit growth in the pressure sensor market.
STMicroelectronics LPS22HB pressure- sensing device is manufactured using a proprietary MEMS technology called “VENSENS”, which allows the pressure sensor to be fabricated on a monolithic silicon chip. The LPS22HB’s sensing element is based on a flexible silicon membrane formed above an air cavity with a controlled gap and defined internal pressure. The membrane is tiny compared to traditional silicon micro-machined membranes. The device is allowing some waterproof functionalities, detailed in the report.
For the LPS22HB, STMicroelectronics has introduced two significant innovations. The first one is a holed cap in silicon, bonded on the sensor to integrate the pressure sensor into a small molded package of 2x2x0.76mm HLGA. This package resembles the one used for the HTS221 humidity sensor. The second one is a spring structure to increase the sensor’s sensitivity and reliability. These two innovations are the core of the new “Bastille” MEMS technology.
This report presents a detailed analysis of the sensor structure and cost, as well as a characteristics comparison with the 1st-generation STMicroelectronics LPS331AP pressure sensor and the Bosch Sensortec BMP280, highlighting differences in each company’s technical choices.
More information on that report at http://www.i-micronews.com/reports.html
The document discusses a fuel nano-additive technology that uses cerium oxide nanoparticles as a fuel borne catalyst. It provides background on nanotechnology and describes how cerium oxide improves fuel combustion efficiency and reduces emissions when mixed into fuel at the nanoscale. Laboratory tests conducted on a diesel engine in Vietnam found that the nano-additive reduced fuel consumption and particulate emissions while increasing combustion pressure over 56 hours of operation with no adverse effects.
Take a look at the fifth generation of EPC’s low voltage transistor
The low voltage GaN device market is increasingly important, and Efficient Power Conversion Corporation (EPC) is a major player in low voltage GaN-on-silicon high-electron-mobility transistor (HEMT) devices. 100V GaN HEMTs are a very new technology but they already compete with silicon transistors, especially in the field of megahertz high frequency applications.
System Plus Consulting has investigated the company’s EPC2045 device, its latest driving 100V for applications such as single-stage 48V converters, USB-C data and power connectors, LiDAR sensors, point-of-load converters and loads in open rack server architectures.
With its new transistor and GaN epitaxy design, the EPC2045 achieves a breakdown voltage of 100V for a current of 16A at 25°C, and a very low RdsOn on-resistance of 7mΩ compared to the previous generation.
The chip-scale packaging of EPC products reduces the final device cost and decreases its inductance, bringing advantages not only with respect to competitors in GaN, but also silicon.
Compared to silicon transistors, GaN process developments have significantly lowered capacitance. This translates into lower gate drive losses and lower device switching losses at higher frequencies for the same on-resistance and voltage rating.
More information on that report at http://www.i-micronews.com/reports.html
The document discusses several topics related to DNA and genetics including DNA replication, restriction enzymes, gel electrophoresis, PCR, DNA sequencing, cloning, and gene expression. It provides figures to illustrate key concepts and techniques such as how restriction enzymes cut DNA, how gel electrophoresis separates DNA fragments by size, how PCR amplifies a target DNA sequence, and the process of cloning a gene into a bacterial plasmid.
The document discusses various types of switching converter topologies used in power supplies such as buck, boost, flyback, and push-pull converters. It then focuses on pulse width modulation (PWM) techniques and current mode PWM controllers, providing information on the UCC38083/4 controller. Examples are given of reference designs and evaluation kits from various manufacturers that use this and other PWM controllers.
Physical and cost analysis of the Bose Audio Amplifier found in the Renault Talisman.
Reverse Costing - Structure, process and cost report - find more here: https://www.systemplus.fr/reverse-costing-reports/bose-automotive-audio-amplifier/
Design of Filter Circuits using MATLAB, Multisim, and ExcelDavid Sandy
The purpose of this project was to design crossover active filter circuits, in order to drive music through three different types of speakers. So, high frequencies would be sent through a Tweeter speaker, low frequencies would be sent through a Woofer speaker, and middle frequencies would be sent through a Midbass driver speaker. Three circuits were created to drive these speakers. Multisim, MATLAB, and Excel, were all used in the design process in order to create the filter circuits correctly.
Circuit Theory 2: Filters Project ReportMichael Sandy
The purpose of this project was to design crossover active filter circuits, in order to drive music through three different types of speakers. So, high frequencies would be sent through a Tweeter speaker, low frequencies would be sent through a Woofer speaker, and middle frequencies would be sent through a Midbass driver speaker. Three circuits were created to drive these speakers. Multisim, MATLAB, and Excel, were all used in the design process in order to create the filter circuits correctly.
Advances In Digital Automation Within RefiningJim Cahill
Emerson's Tim Olsen presents to Argentinean refiners on the changes in automation technologies and how they are being applied to improve efficiency and reduce costs.
Poster at EMBL: Diagnosis and monitoring of Leptomeningeal Disease using Circ...Ronak Shah
This document describes a study that used circulating cell-free DNA (cfDNA) isolated from cerebrospinal fluid (CSF) to diagnose and monitor leptomeningeal disease. The researchers used a targeted sequencing panel to analyze 341 cancer genes in cfDNA from 53 patients. Results from CSF cfDNA analysis were compared to standard CSF cytopathology and MRI findings. CSF cfDNA analysis detected tumor-derived genetic alterations and was more sensitive than cytopathology. The study demonstrates that genomic analysis of CSF cfDNA can help facilitate early diagnosis of central nervous system tumors and guide treatment.
The IMPACT of INDEL realignment: Detecting insertions and deletions longer th...Ronak Shah
Cancer is a disease of the genome –most of its forms result from a buildup of genetic alterations that, directly or indirectly, allow the patient’s cells to proliferate without restraint. For decades, identifying and targeting cancer mutations for treatment was impractical due to the limitations of sequencing technology. However, the rise of high-throughput next-generation sequencing (NGS) tools has allowed researchers to rapidly and cheaply sequence large, targeted regions of DNA. MSK-IMPACT(Memorial Sloan Kettering-IntegratedMutation Profiling of Actionable Cancer Targets), a sequencing platform with an associated computational pipeline, takes advantage of improvements in sequencing technology to analyzetumor specimensfor clinically actionable variants in341 cancer-associatedgenes.Criticalto IMPACT’s efficacy is the detection of somatic DNAalterationslike INDELs, which are insertions or deletions of nucleotides. Current sequence aligners have difficulty accuratelymapping reads (short, overlapping DNA sequences) containing morethan a single base change, let alone reads containing INDELs. This flaw necessitates the use of INDEL realigners, whichrearrange reads inregions where INDELs might exist in order to identify them more easily. Currently, the INDEL realignment software associated withMSK-IMPACT’scomputational pipeline, the Genome Analysis Toolkit’s IndelRealigner (GATK), canonly efficiently resolveINDELsshorter than 30 base pairs, which limits theplatform’sreliability forINDELdetection. Thus, wetested and compared the performance of a new INDEL realigner called ABRA (Assembly BasedRe-Aligner) to that of GATK’s IndelRealigner.
Detecting clinically actionable somatic structural aberrations from targeted ...Ronak Shah
Structural aberrations including deletions, insertions, inversions, tandem duplications, translocations, and more complex rearrangements constitute a frequent type of alteration in human tumors. Here, we sought to explore the potential to discover such events from targeted DNA sequence data in our CLIA-compliant molecular diagnostics laboratory. To detect somatic structural aberrations in individual tumors, we have developed an analytic framework in Perl & Python to detect these events in data generated by a hybridization capture-based, targeted sequencing clinical assay (MSK-IMPACT), which can reveal structural rearrangements as small as 500bp.
Developing a framework for for detection of low frequency somatic genetic alt...Ronak Shah
Cancer is a complex, heterogeneous disease of the genome. Most cancers result
from an accumulation of multiple genetic alterations that lead to dysfunction of cancer-associated
genes and pathways. Recent advances in sequencing technology have enabled comprehensive
profiling of genetic alterations in cancer. We have established a targeted sequencing platform
(IMPACT: Integrated Mutation Profiling of Actionable Cancer Targets) using hybridization capture and
next-generation sequencing (NGS) technology, which can reveal mutations, indels and copy number
alterations involving 340 cancer related genes.
Protein-Protein Interaction using SVM based kernel,Jacob Coefficient and Gene...Ronak Shah
Protein-Protein interactions discovered by the existing high-throughput techniques contain very high amount of false positives. Here we present an SVM based approach to generate a model that is built on sequence and non-sequence based information of the interacting proteins. This model is used to assess the reliability of given protein-protein interactions. It was run on the interaction data of a pathogenic bacterium; Treponema pallidum (causes Syphilis in humans) obtained from Yeast two hybrid experiments. Various kernels were used for building the model and of all, Sigmoid kernel performed well when used with all the features combined with area under the receiver operating curve (ROC) as 0.53.
GraphRAG for Life Science to increase LLM accuracyTomaz Bratanic
GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
leewayhertz.com-AI in predictive maintenance Use cases technologies benefits ...alexjohnson7307
Predictive maintenance is a proactive approach that anticipates equipment failures before they happen. At the forefront of this innovative strategy is Artificial Intelligence (AI), which brings unprecedented precision and efficiency. AI in predictive maintenance is transforming industries by reducing downtime, minimizing costs, and enhancing productivity.
Driving Business Innovation: Latest Generative AI Advancements & Success StorySafe Software
Are you ready to revolutionize how you handle data? Join us for a webinar where we’ll bring you up to speed with the latest advancements in Generative AI technology and discover how leveraging FME with tools from giants like Google Gemini, Amazon, and Microsoft OpenAI can supercharge your workflow efficiency.
During the hour, we’ll take you through:
Guest Speaker Segment with Hannah Barrington: Dive into the world of dynamic real estate marketing with Hannah, the Marketing Manager at Workspace Group. Hear firsthand how their team generates engaging descriptions for thousands of office units by integrating diverse data sources—from PDF floorplans to web pages—using FME transformers, like OpenAIVisionConnector and AnthropicVisionConnector. This use case will show you how GenAI can streamline content creation for marketing across the board.
Ollama Use Case: Learn how Scenario Specialist Dmitri Bagh has utilized Ollama within FME to input data, create custom models, and enhance security protocols. This segment will include demos to illustrate the full capabilities of FME in AI-driven processes.
Custom AI Models: Discover how to leverage FME to build personalized AI models using your data. Whether it’s populating a model with local data for added security or integrating public AI tools, find out how FME facilitates a versatile and secure approach to AI.
We’ll wrap up with a live Q&A session where you can engage with our experts on your specific use cases, and learn more about optimizing your data workflows with AI.
This webinar is ideal for professionals seeking to harness the power of AI within their data management systems while ensuring high levels of customization and security. Whether you're a novice or an expert, gain actionable insights and strategies to elevate your data processes. Join us to see how FME and AI can revolutionize how you work with data!
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
Main news related to the CCS TSI 2023 (2023/1695)Jakub Marek
An English 🇬🇧 translation of a presentation to the speech I gave about the main changes brought by CCS TSI 2023 at the biggest Czech conference on Communications and signalling systems on Railways, which was held in Clarion Hotel Olomouc from 7th to 9th November 2023 (konferenceszt.cz). Attended by around 500 participants and 200 on-line followers.
The original Czech 🇨🇿 version of the presentation can be found here: https://www.slideshare.net/slideshow/hlavni-novinky-souvisejici-s-ccs-tsi-2023-2023-1695/269688092 .
The videorecording (in Czech) from the presentation is available here: https://youtu.be/WzjJWm4IyPk?si=SImb06tuXGb30BEH .
This presentation provides valuable insights into effective cost-saving techniques on AWS. Learn how to optimize your AWS resources by rightsizing, increasing elasticity, picking the right storage class, and choosing the best pricing model. Additionally, discover essential governance mechanisms to ensure continuous cost efficiency. Whether you are new to AWS or an experienced user, this presentation provides clear and practical tips to help you reduce your cloud costs and get the most out of your budget.
A Comprehensive Guide to DeFi Development Services in 2024Intelisync
DeFi represents a paradigm shift in the financial industry. Instead of relying on traditional, centralized institutions like banks, DeFi leverages blockchain technology to create a decentralized network of financial services. This means that financial transactions can occur directly between parties, without intermediaries, using smart contracts on platforms like Ethereum.
In 2024, we are witnessing an explosion of new DeFi projects and protocols, each pushing the boundaries of what’s possible in finance.
In summary, DeFi in 2024 is not just a trend; it’s a revolution that democratizes finance, enhances security and transparency, and fosters continuous innovation. As we proceed through this presentation, we'll explore the various components and services of DeFi in detail, shedding light on how they are transforming the financial landscape.
At Intelisync, we specialize in providing comprehensive DeFi development services tailored to meet the unique needs of our clients. From smart contract development to dApp creation and security audits, we ensure that your DeFi project is built with innovation, security, and scalability in mind. Trust Intelisync to guide you through the intricate landscape of decentralized finance and unlock the full potential of blockchain technology.
Ready to take your DeFi project to the next level? Partner with Intelisync for expert DeFi development services today!
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
5th LF Energy Power Grid Model Meet-up SlidesDanBrown980551
5th Power Grid Model Meet-up
It is with great pleasure that we extend to you an invitation to the 5th Power Grid Model Meet-up, scheduled for 6th June 2024. This event will adopt a hybrid format, allowing participants to join us either through an online Mircosoft Teams session or in person at TU/e located at Den Dolech 2, Eindhoven, Netherlands. The meet-up will be hosted by Eindhoven University of Technology (TU/e), a research university specializing in engineering science & technology.
Power Grid Model
The global energy transition is placing new and unprecedented demands on Distribution System Operators (DSOs). Alongside upgrades to grid capacity, processes such as digitization, capacity optimization, and congestion management are becoming vital for delivering reliable services.
Power Grid Model is an open source project from Linux Foundation Energy and provides a calculation engine that is increasingly essential for DSOs. It offers a standards-based foundation enabling real-time power systems analysis, simulations of electrical power grids, and sophisticated what-if analysis. In addition, it enables in-depth studies and analysis of the electrical power grid’s behavior and performance. This comprehensive model incorporates essential factors such as power generation capacity, electrical losses, voltage levels, power flows, and system stability.
Power Grid Model is currently being applied in a wide variety of use cases, including grid planning, expansion, reliability, and congestion studies. It can also help in analyzing the impact of renewable energy integration, assessing the effects of disturbances or faults, and developing strategies for grid control and optimization.
What to expect
For the upcoming meetup we are organizing, we have an exciting lineup of activities planned:
-Insightful presentations covering two practical applications of the Power Grid Model.
-An update on the latest advancements in Power Grid -Model technology during the first and second quarters of 2024.
-An interactive brainstorming session to discuss and propose new feature requests.
-An opportunity to connect with fellow Power Grid Model enthusiasts and users.
Salesforce Integration for Bonterra Impact Management (fka Social Solutions A...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on integration of Salesforce with Bonterra Impact Management.
Interested in deploying an integration with Salesforce for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
Monitoring and Managing Anomaly Detection on OpenShift.pdfTosin Akinosho
Monitoring and Managing Anomaly Detection on OpenShift
Overview
Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices.
Key Topics Covered
1. Introduction to Anomaly Detection
- Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems.
2. Understanding Edge (IoT)
- Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source.
3. What is ArgoCD?
- Discover ArgoCD, a declarative, GitOps continuous delivery tool for Kubernetes, and its role in deploying applications on edge devices.
4. Deployment Using ArgoCD for Edge Devices
- Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD.
5. Introduction to Apache Kafka and S3
- Explore Apache Kafka for real-time data streaming and Amazon S3 for scalable storage solutions.
6. Viewing Kafka Messages in the Data Lake
- Learn how to view and analyze Kafka messages stored in a data lake for better insights.
7. What is Prometheus?
- Get to know Prometheus, an open-source monitoring and alerting toolkit, and its application in monitoring edge devices.
8. Monitoring Application Metrics with Prometheus
- Detailed instructions on setting up Prometheus to monitor the performance and health of your anomaly detection system.
9. What is Camel K?
- Introduction to Camel K, a lightweight integration framework built on Apache Camel, designed for Kubernetes.
10. Configuring Camel K Integrations for Data Pipelines
- Learn how to configure Camel K for seamless data pipeline integrations in your anomaly detection workflow.
11. What is a Jupyter Notebook?
- Overview of Jupyter Notebooks, an open-source web application for creating and sharing documents with live code, equations, visualizations, and narrative text.
12. Jupyter Notebooks with Code Examples
- Hands-on examples and code snippets in Jupyter Notebooks to help you implement and test anomaly detection models.
Introduction of Cybersecurity with OSS at Code Europe 2024Hiroshi SHIBATA
I develop the Ruby programming language, RubyGems, and Bundler, which are package managers for Ruby. Today, I will introduce how to enhance the security of your application using open-source software (OSS) examples from Ruby and RubyGems.
The first topic is CVE (Common Vulnerabilities and Exposures). I have published CVEs many times. But what exactly is a CVE? I'll provide a basic understanding of CVEs and explain how to detect and handle vulnerabilities in OSS.
Next, let's discuss package managers. Package managers play a critical role in the OSS ecosystem. I'll explain how to manage library dependencies in your application.
I'll share insights into how the Ruby and RubyGems core team works to keep our ecosystem safe. By the end of this talk, you'll have a better understanding of how to safeguard your code.
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
4. ILLUMINA INPUT DATA: 20BN BASE PAIR,
180MN READS, 148X COVERAGE
Read
Read
Type
Read
Len
(Mean)
Insert
Size
Total bases
Total
( read pairs)
Total
( reads)
Estimated
Coverage
(X)
Hiseq Paired End 100 400 3,168,468,000 15,842,340 31,684,680 22
Hiseq Paired End 100 400 3,320,637,800 16,603,189 33,206,378 23
Hiseq Paired End 100 400 3,238,613,000 16,193,065 32,386,130 23
Hiseq
Short
Overlap
merged
178 335 2,211,006,384 12,401,099 16
Hiseq
Short
Overlap
merged
178 335 2,209,098,067 12,391,800 16
Hiseq
Short
Overlap
merged
178 335 2,178,151,877 12,215,609 15
Hiseq
Short
Overlap
unmerged
100 335 1,550,423,600 15,504,236 11
Hiseq
Short
Overlap
unmerged
100 335 1,551,440,000 15,514,400 11
Hiseq
Short
Overlap
unmerged
100 335 1,519,735,600 15,197,356 11
Total 20,947,574,328 48,638,594 180,501,688 148
CLC-Bio
Input
20,947,574,328 180,501,688
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5. SEDUM ILLUMINA REFERENCE
FLOWCYTOMETRY GENOME SIZE: 142MB ESTIMATED GENOME SIZE: 180MB CURRENT
GENOME SIZE: 255MB N50(SCAFFOLD): 2.8KB N50(CONTIG): 1.6KB
Scaffolding Stats Contigs Stats
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Number of scaffolds 219,455
Total size of scaffolds 267,197,078
Total scaffold length as percentage of
assumed genome size
2
Longest scaffold 124,757
Shortest scaffold 200
Number of scaffolds > 1K nt 63,451 28.90%
Number of scaffolds > 10K nt 2,498 1.10%
Number of scaffolds > 100K nt 1 0.00%
Mean scaffold size 1,218
Median scaffold size 464
N50 scaffold length 2,848
Percentage of assembly in scaffolded
contigs
52.40%
Percentage of assembly in
unscaffolded contigs
47.60%
Average number of contigs per
scaffold
1.3
Average length of break (>25 Ns)
between contigs in scaffold
162
Number of
contigs
292,607
Number of
contigs in
scaffolds
113,984
Number of
contigs not in
scaffolds
178,623
Total size of
contigs
255,346,080
Longest contig 56,108
Shortest contig 176
Number of
contigs > 1K nt
67,774 23.20%
Number of
contigs > 10K nt
641 0.20%
Mean contig
size
873
Median contig
size
412
N50 contig
length
1,615
6. ION TORRENT 400 BP CHIP
READ ANALYSIS
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7. ION TORRENT INPUT DATA: 5BN BASE
PAIR, 19MN READS, 37X COVERAGE
Read Read Type
Read
Len
(Mean)
Total bases Total reads
Estimated
Coverage
(X)
Ion Torrent 400bp chip 286 897,163,323 3,130,643 6
Ion Torrent 400bp chip 241 931,376,271 3,850,295 7
Ion Torrent 400bp chip 269 1,113,089,592 4,126,822 8
Ion Torrent 400bp chip 252 1,098,412,220 4,350,400 8
Ion Torrent 400bp chip 274 1,207,920,840 4,408,077 9
Total 5,247,962,246 19,866,237 37
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8. ALIGNERS USED: BWASW AND TMAP
Parameters used in both aligners were default.
Where for both:
Mismatch penalty:3
Gap open penalty: 5
Gap extension penalty:2
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9. MERGED BWA RESULTS: 25% INSERTION
RATE; 33% DELETION RATE; 85%MISTMATCH
Mapping Results
reads 23,277,245
mapped reads 21,124,134
mapped bases 3,622,712,040
perfectly mapped 3,143,328
len max 433
len mean 171
len stdev 82
mapq mean 95
mapq stdev 87
snp rate 4
ins rate 25
del rate 33
pct mismatch 85
base qual mean 22
base qual stdev 9
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10. MERGED BWA RESULTS: 91% READS MAPPED
Total Number of Reads: 23.3M
Number of Reads Mapped:21.1M
Percentage of Reads Mapped: 91%
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11. MERGED BWA RESULTS: BASE QUALITY
DECREASES FROM 100 BP
Mean Base Quality
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Quality
keeps on
dropping
after 100bp
12. MERGED BWA RESULTS: BASE QUALITY
DECREASES FROM 100 BP
Per Base Quality
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13. MERGED BWA RESULTS: LOW ERRORS AT THE
START; HIGH ERRORS AT THE END
Error Profiles:
The profiles indicate that the Mismatch, Insertion
and Deletion are really high and they tend to be low
at the start of the sequence and keep on increasing
gradually as the sequence gets longer.
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14. MERGED BWA RESULTS: HIGH MISMATCH,
HIGH INSERTION; HIGH DELETION
Error Profiles
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15. MERGED BWA RESULTS: HIGH MISMATCH,
HIGH INSERTION; HIGH DELETION
Error Profiles
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16. MERGED BWA RESULTS: OVER REPRESENTATION
BETWEEN 150-450 BP
K-mer Profile
There is over representation of K-mers from position
150 to 450.
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17. MERGED TMAP RESULTS : 28% INSERTION
34% DELETION; 88% MISMATCH
Mapping Results
reads 19,866,237
mapped reads 17,795,383
mapped bases 3,381,672,736
perfectly mapped 2,053,578
len max 433
len mean 190
len stdev 79
maq mean 14
maq stdev 10
snp rate 5%
ins rate 28%
del rate 34%
pct mismatch 88%
base qual mean 22
base qual stdev 9
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18. MERGED TMAP RESULTS: 90% READ MAPPED
Total Number of Reads: 17.8M
Number of Reads Mapped:19.9M
Percentage of Reads Mapped: 90%
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19. MERGED TMAP RESULTS: BASE QUALITY
DECREASES FROM 100 BP
Mean Base Quality
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Quality
keeps on
dropping
after 100
bp
20. MERGED TMAP RESULTS: BASE QUALITY
DECREASES FROM 100 BP
Per Base Quality
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21. MERGED TMAP RESULTS: HIGH MISMATCH,
HIGH INSERTION; HIGH DELETION
Error Profiles
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22. MERGED TMAP RESULTS: HIGH MISMATCH,
HIGH INSERTION; HIGH DELETION
Error Profiles
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23. MERGED TMAP RESULTS: OVER
REPRESENTATION BETWEEN 150-450 BP
K-mer Profile
There is over representation of K-mers from position
150 to 450.
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25. ION TORRENT INPUT DATA: 13BN BASE
PAIR, 72MN READS, 95X COVERAGE
Read Read Type
Read
Len
(Mean)
Total bases
Total
reads
Estimated
Coverage
(X)
Ion Torrent
ORG
100bp,
200bp
400bp chip
187 13,521,610,812 72,058,773 95
Ion Torrent
Corrected
100bp,
200bp
400bp chip
187 13,479,341,388
72,058,773
95
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26. ORG BWA RESULTS: 21% INSERTION; 27%
DELETION; 81% MISMATCH
CORRECTED BWA RESULTS: 10% INSERTION; 15%
DELETION; 70% MISMATCH
Corrected BWA Mapping Results
reads 79,986,695
mapped reads 75,639,986
mapped bases 14,695,848,107
perfectly mapped 23,006,719
len max 678
len mean 194
len stdev 83
mapq mean 100
mapq stdev 88
snp rate 2%
ins rate 10%
del rate 15%
pct mismatch 70%
base qual mean 20
base qual stdev 6
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ORG BWA Mapping Results
reads 80,098,562
mapped reads 71611630
mapped bases 10,456,280,566
perfectly mapped 13,729,260
len max 433
len mean 146
len stdev 66
mapq mean 97
mapq stdev 86
snp rate 3.2%
ins rate 21%
del rate 27%
pct mismatch 81%
base qual mean 21
base qual stdev 6
27. ORG BWA RESULTS: 89% READ MAPPED
CORRECTED BWA RESULTS: 95% READS MAPPED
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ORG BWA Mapping Results
Total Number of Reads 80.9M
Number of Reads Mapped 71.6M
Percentage of Reads Mapped 89%
Corrected BWA Mapping Results
Total Number of Reads 80.0M
Number of Reads Mapped 75.6M
Percentage of Reads Mapped 95%
28. CORRECTED BWA RESULTS: BASE QUALITY
DECREASE FROM 100
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Quality
keeps on
dropping
after 100
bp
29. CORRECTED BWA RESULTS : BASE QUALITY
DECREASES FROM 100 BP
Per Base Quality
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30. CORRECTED BWA RESULTS: HIGH MISMATCH; HIGH INSERTION;
HIGH DELETION; BUT 10% SMALLER THEN ORG READS
Error Profiles
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31. CORRECTED BWA RESULTS: HIGH MISMATCH; HIGH INSERTION;
HIGH DELETION; BUT 10% SMALLER THEN ORG READS
Error Profiles
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32. CORRECTED BWA RESULTS: OVER
REPRESENTATION BETWEEN 150-450 BP
K-mer Profile
There is over representation of K-mers from position
250 to 450.
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33. ORG TMAP RESULTS: 20% INSERTION; 23%
DELETION; 84% MISMATCH
CORRECTED TMAP RESULTS: 13% INSERTION;
18% DELETION; 74% MISMATCH
Corrected TMAP Mapping Results
reads 72,058,773
mapped reads 68,116,303
mapped bases 12,763,573,084
perfectly mapped 18,029,367
len max 678
len mean 187
len stdev 81
mapq mean 13
mapq stdev 10
snp rate 3
ins rate 13
del rate 18
pct mismatch 74
base qual mean 20
base qual stdev 6
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ORG TMAP Mapping Results
reads 72,058,773
mapped reads 65,224,903
mapped bases 12,211,168,843
perfectly mapped 10,436,368
len max 638
len mean 187
len stdev 81
mapq mean 14
mapq stdev 10
snp rate 3
ins rate 20
del rate 23
pct mismatch 84
base qual mean 20
base qual stdev 6
34. ORG TMAP RESULTS: 89% READ MAPPED
CORRECTED TMAP RESULTS: 95% READS
MAPPED
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ORG BWA Mapping Results
Total Number of Reads 72.1M
Number of Reads Mapped 65.2M
Percentage of Reads Mapped 91%
Corrected BWA Mapping Results
Total Number of Reads 72.1M
Number of Reads Mapped 68.1M
Percentage of Reads Mapped 95%
35. CORRECTED TMAP RESULTS: BASE QUALITY
DECREASE FROM 100
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Quality
keeps on
dropping
after 200
bp
36. CORRECTED TMAP RESULTS : BASE
QUALITY DECREASES FROM 100 BP
Per Base Quality
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37. CORRECTED TMAP RESULTS: HIGH MISMATCH; HIGH INSERTION;
HIGH DELETION; BUT 10% SMALLER THEN ORG READS
Error Profiles
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38. CORRECTED TMAP RESULTS: HIGH MISMATCH; HIGH INSERTION;
HIGH DELETION; BUT 10% SMALLER THEN ORG READS
Error Profiles
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39. CORRECTED TMAP RESULTS : OVER
REPRESENTATION BETWEEN 150-450 BP
K-mer Profile
There is over representation of K-mers from position
150 to 450.
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41. 400 BP READS: N50 421BP; MAX CONTIG 4.6KB;
TOTAL BASES 201MB
400 Bp Reads Assembly Stats
Number of contigs 51,7835
Total size of contigs 201,990,292
Longest contig 4,684
Shortest contig 23
Number of contigs > 1K nt 11,939 2.30%
Number of contigs > 10K nt 0 0.00%
Mean contig size 390
Median contig size 329
N50 contig length 421
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42. 400 BP READS: N50 426BP; MAX CONTIG 4.2KB;
TOTAL BASES 201MB
400 Bp Reads clipped at length 450 Assembly Stats
Number of contigs 509,308
Total size of contigs 201,527,141
Longest contig 4,272
Shortest contig 23
Number of contigs > 1K nt 13,781 2.70%
Number of contigs > 10K nt 0 0.00%
Mean contig size 396
Median contig size 331
N50 contig length 426
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• Reads Clipped at length 450
43. 400 BP READS: N50 430BP; MAX CONTIG 5.4KB;
TOTAL BASES 192MB
400 Bp Reads clipped at length 450 qual 15 Assembly Stats
Number of contigs 478,037
Total size of contigs 192,109,210
Longest contig 5,378
Shortest contig 23
Number of contigs > 1K nt 16,737 3.50%
Number of contigs > 10K nt 0 0.00%
Mean contig size 402
Median contig size 324
N50 contig length 430
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• Reads Clipped at length 450 with minimum quality of 15
44. ORG READS: N50 397BP; MAX CONTIG 5KB;
TOTAL BASES 185MB
Org Reads Assembly Stats
Number of contigs 486,255
Total size of contigs 185,584,458
Longest contig 5,878
Shortest contig 24
Number of contigs > 1K nt 15,386 3.20%
Number of contigs > 10K nt 0 0.00%
Mean contig size 382
Median contig size 299
N50 contig length 397
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45. ERROR CORRECTED READS: N50 550BP;
MAX CONTIG 28KB; TOTAL BASES 203MB
Error Corrected Reads Assembly Stats
Number of contigs 424,264
Total size of contigs 203,921,151
Longest contig 28,009
Shortest contig 24
Number of contigs > 1K nt 33,025 7.80%
Number of contigs > 10K nt 43 0.00%
Mean contig size 481
Median contig size 328
N50 contig length 550
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