The document discusses nanopore sequencing technology. It provides an overview of nanopore sequencing, including that Oxford Nanopore became the first company to provide a commercially available nanopore sequencer in 2015. It also discusses the raw nanopore sequencing data and some of the initial processing steps needed to transform the raw data, with the goal of producing a basecaller to predict genomic bases from the data. Future directions for improving nanopore sequencing are also mentioned.
Nanopore sequencing is a unique, scalable technology that enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence.
This document discusses nanopore sequencing technology. It provides an overview of nanopore sequencing, including what nanopore sequencing is, the types of nanopores used (biological and solid state), advantages such as not requiring amplification or labeling, and challenges with processing large amounts of raw data. The document then examines raw nanopore data and the initial steps needed to process the data, including creating a training data set to predict genomic bases and releasing analysis packages to the community.
A new method of Nucleic Acid Sequencing using Nanotechnological Advances with Advantage of Single molecule sequencing, low cost and time requirement, easy to handle
This document provides an overview of nanopore sensors and their applications. It discusses biological nanopores formed by pore-forming proteins, solid state nanopores fabricated in materials like silicon nitride, and hybrid nanopores combining biological and solid state elements. The document outlines several applications of nanopore sensors including DNA sequencing, detection of DNA damage, analysis of circulating microRNAs for cancer detection, and single-molecule protein studies. It also discusses the potential of solid state nanopores integrated with nanowire field-effect transistors and hybrid nanopores for improved specificity.
Nanopore DNA sequencing is a fourth generation sequencing technique that involves passing single strands of DNA through a nanopore and detecting changes in electrical current caused by each nucleotide base. There are two main types of nanopores - biological nanopores which are protein channels inserted into membranes, and solid-state nanopores fabricated in thin materials like silicon nitride or graphene. Some examples of biological nanopores used for sequencing are the alpha-hemolysin pore and the MspA pore. Nanopore sequencing has advantages over other techniques in being label-free, capable of very long reads, and requiring low sample amounts. However, challenges remain in slowing DNA translocation for higher resolution and reducing noise in the electrical signals.
Biotechnophysics: DNA Nanopore SequencingMelanie Swan
Biophysics (not merely bioengineering) is required to understand the fundamental mechanisms of biology in order to make technologies (bench and bioinformatic) for understanding them
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
Nanopore sequencing is a unique, scalable technology that enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence.
This document discusses nanopore sequencing technology. It provides an overview of nanopore sequencing, including what nanopore sequencing is, the types of nanopores used (biological and solid state), advantages such as not requiring amplification or labeling, and challenges with processing large amounts of raw data. The document then examines raw nanopore data and the initial steps needed to process the data, including creating a training data set to predict genomic bases and releasing analysis packages to the community.
A new method of Nucleic Acid Sequencing using Nanotechnological Advances with Advantage of Single molecule sequencing, low cost and time requirement, easy to handle
This document provides an overview of nanopore sensors and their applications. It discusses biological nanopores formed by pore-forming proteins, solid state nanopores fabricated in materials like silicon nitride, and hybrid nanopores combining biological and solid state elements. The document outlines several applications of nanopore sensors including DNA sequencing, detection of DNA damage, analysis of circulating microRNAs for cancer detection, and single-molecule protein studies. It also discusses the potential of solid state nanopores integrated with nanowire field-effect transistors and hybrid nanopores for improved specificity.
Nanopore DNA sequencing is a fourth generation sequencing technique that involves passing single strands of DNA through a nanopore and detecting changes in electrical current caused by each nucleotide base. There are two main types of nanopores - biological nanopores which are protein channels inserted into membranes, and solid-state nanopores fabricated in thin materials like silicon nitride or graphene. Some examples of biological nanopores used for sequencing are the alpha-hemolysin pore and the MspA pore. Nanopore sequencing has advantages over other techniques in being label-free, capable of very long reads, and requiring low sample amounts. However, challenges remain in slowing DNA translocation for higher resolution and reducing noise in the electrical signals.
Biotechnophysics: DNA Nanopore SequencingMelanie Swan
Biophysics (not merely bioengineering) is required to understand the fundamental mechanisms of biology in order to make technologies (bench and bioinformatic) for understanding them
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
The document summarizes a coarse-grained molecular dynamics simulation of DNA translocation through a nanopore. Two nanopore systems were modeled (System A and B) with different pore geometries and sizes. Snapshots from the simulations showed DNA conformations outside, during capture, and inside the pore. Plots of the DNA center of mass over time demonstrated capture and translocation. The simulations provided insight into how DNA bending and stretching occurs during translocation and how pore size and shape can influence the process.
Ultra-long read methods for nanopore single molecule sequencingscalene
This document discusses ultra-long read nanopore sequencing. It notes that reads approaching 1 Mbp have been reported, which could enable complete assembly of a human genome within years. Sample preparation is critical for ultra-long reads, as DNA shears easily. Transposase libraries produce better ultra-long reads than ligation libraries. An E. coli dataset using a phenol/chloroform library with reads over 500 kb achieved 1x coverage. Comparison of read sets showed ultra-long reads improved assembly N50 significantly. Future work includes improving yield through molecule enrichment and enabling routine generation of ultra-long reads for metagenomes.
This document discusses nanopore sequencing technology from Oxford Nanopore Technologies. It provides details on their MinION and PromethION sequencing devices, including the design of the MinION flow cell and basecalling process. It also describes the MinION Access Program (MAP) and MinION Analysis and Reference Consortium (MARC) for evaluating and improving the nanopore sequencing platform. While showing promise, the document notes some areas still needing improvement for the technology to be fully ready for production, including flow cell quality and throughput.
This presentation provides an overview of next generation sequencing (NGS). It discusses the history of DNA sequencing, from early methods like Maxam-Gilbert sequencing and Sanger sequencing, to newer technologies like 454 sequencing, Illumina sequencing, and Ion Torrent sequencing. These NGS methods allow for massively parallel sequencing of many DNA fragments to generate millions of short reads. The presentation outlines the types of NGS instruments and their applications in fields like molecular biology, medicine, and forensics. It also discusses future challenges in DNA sequencing and decreasing costs to analyze more human genomes.
Next generation-sequencing.ppt-convertedShweta Tiwari
The advance version, sequences the whole genome efficiently with high speed and high throughput sequencing at reduce cost is termed as Next Generation Sequencing (NGS) or massively parallel sequencing (MPS).
Next Generation Sequencing (NGS) Is A Modern And Cost Effective Sequencing Technology Which Enables Scientists To Sequence Nucleic Acids At Much Faster Rate. In This Presentation, You Will Learn About What is NGS, Idea Behind NGS, Methodology And Protocol, Widely Adapted NGS Protocols, Applications And References For Further Study.
A full picture of -omics cellular networks of regulation brings researchers closer to a realistic and reliable understanding of complex conditions. For more information, please visit: http://tbioinfopb.pine-biotech.com/
White Paper: Next-Generation Genome Sequencing Using EMC Isilon Scale-Out NAS...EMC
This EMC Isilon sizing and performance guideline White Paper reviews the Key Performance Indicators (KPIs) that most strongly impact the production processes for the storage of data from Next-Generation Sequencing (NGS) workflows.
The SOLiD 3 System provides high throughput DNA sequencing with several advantages over other technologies:
- It can sequence entire transcriptomes without any gaps, determine strand-specific expression patterns, and detect SNPs with low false positives.
- Applications include assessing DNA-protein interactions across multiple samples, discovering novel transcripts and splice variants without microarray bias, and characterizing structural rearrangements.
- The system uses emulsion PCR to clonally amplify template beads, followed by deposition of modified beads on a flow cell and sequencing by ligation using fluorescently labeled di-base probes.
Next-generation sequencing course, part 1: technologiesJan Aerts
This document provides an overview of next-generation sequencing technologies and their applications. It discusses genome enrichment techniques to isolate targeted regions for sequencing. It also describes template preparation methods like emulsion PCR and solid-phase amplification. Finally, it reviews various sequencing platforms like Illumina, SOLiD, 454 and details the sequencing and imaging processes. There are exercises proposed to work with sequencing data files in Galaxy.
RNASeq - Analysis Pipeline for Differential ExpressionJatinder Singh
RNA-Seq is a technique that uses next generation sequencing to sequence RNA transcripts and quantify gene expression levels. It can be used to estimate transcript abundance, detect alternative splicing, and compare gene expression profiles between healthy and diseased tissue. Computational challenges include read mapping due to exon-exon junctions and normalization of read counts. Key steps in RNA-Seq analysis include read mapping, transcript assembly, counting and normalizing reads, and detecting differentially expressed genes.
CSU Next Generation Sequencing Core 06/09/2015Richard Casey
The Next Generation Sequencing Core at Colorado State University provides next generation sequencing and bioinformatics services and support using Illumina and Ion Torrent sequencing platforms for applications such as DNA sequencing, RNA sequencing, epigenetics, metagenomics, and more, drawing on over 10 years of experience and resources including on-campus laboratories, computational infrastructure, and staff expertise. Services include laboratory preparation, sequencing runs, bioinformatics analysis, and training.
This document discusses computational methods and challenges for genome assembly using next-generation sequencing data. It describes the four main stages of genome assembly as preprocessing filtering, graph construction, graph simplification, and postprocessing filtering. Each stage processes the data from the previous stage to build the assembly graph and reduce complexity, though some assemblers delay filtering steps.
This document provides an overview of DNA microarrays (DNA chips), including:
1. It describes how DNA microarrays work, the basic components and steps involved including manufacturing probes, sample preparation, hybridization, scanning, and data analysis.
2. It discusses the two main types of microarrays - cDNA microarrays produced by robotic spotting and oligonucleotide arrays produced by in situ synthesis.
3. It outlines some of the applications of DNA microarrays including analyzing gene expression, disease classification, toxicogenomics, and more.
Slide Deck from Josh's 2014 presentation at the Illumina user group meeting in RTP. Slides describe our experience with V3 and V4 chemistries on a very large cohort of exome sequenced samples.
The document discusses DNA microarrays, including their applications, history, major steps, methods of construction, and technical issues. DNA microarrays allow analysis of gene expression across thousands of genes simultaneously. They have been used since the 1990s and are constructed by attaching DNA probes to a solid surface in a high-density array. Two main types are cDNA-based microarrays using amplified cDNA and oligonucleotide-based arrays like Affymetrix GeneChips containing short DNA sequences.
The document provides information about a presentation on bioinformatics and DNA sequencing. It includes 5 sections written by different group members. The summary is:
The presentation discusses DNA sequencing methods including Sanger sequencing. It describes the DNA sequencing process which involves separating newly synthesized DNA strands by length using heating and loading them into a capillary tube, passing the strands through a laser beam to cause dye fluorescence detected by a photocell, and computers interpreting the color sequence. Modern applications of sequencing include forensics, medicine, and agriculture.
Nanopore sequencing is a technique that determines DNA sequences by passing DNA fragments through a protein pore. It has the advantages of a small sequencer size, long read lengths, and potential for direct RNA sequencing. However, the raw nanopore data is complex and requires processing to transform it into usable genomic sequence information. The document discusses the nanopore sequencing technology, characteristics of the raw data, steps to process the raw data into a training dataset to predict genomic bases, and future directions for the technology.
DNA sequencing determines the order of nucleotides in a DNA segment. The first generation methods developed in 1977 were Maxam-Gilbert and Sanger sequencing, with Sanger becoming the most common. Next generation sequencing now includes Illumina, which is the most widely used, as well as PacBio and Nanopore third generation real-time single molecule techniques.
The document summarizes a coarse-grained molecular dynamics simulation of DNA translocation through a nanopore. Two nanopore systems were modeled (System A and B) with different pore geometries and sizes. Snapshots from the simulations showed DNA conformations outside, during capture, and inside the pore. Plots of the DNA center of mass over time demonstrated capture and translocation. The simulations provided insight into how DNA bending and stretching occurs during translocation and how pore size and shape can influence the process.
Ultra-long read methods for nanopore single molecule sequencingscalene
This document discusses ultra-long read nanopore sequencing. It notes that reads approaching 1 Mbp have been reported, which could enable complete assembly of a human genome within years. Sample preparation is critical for ultra-long reads, as DNA shears easily. Transposase libraries produce better ultra-long reads than ligation libraries. An E. coli dataset using a phenol/chloroform library with reads over 500 kb achieved 1x coverage. Comparison of read sets showed ultra-long reads improved assembly N50 significantly. Future work includes improving yield through molecule enrichment and enabling routine generation of ultra-long reads for metagenomes.
This document discusses nanopore sequencing technology from Oxford Nanopore Technologies. It provides details on their MinION and PromethION sequencing devices, including the design of the MinION flow cell and basecalling process. It also describes the MinION Access Program (MAP) and MinION Analysis and Reference Consortium (MARC) for evaluating and improving the nanopore sequencing platform. While showing promise, the document notes some areas still needing improvement for the technology to be fully ready for production, including flow cell quality and throughput.
This presentation provides an overview of next generation sequencing (NGS). It discusses the history of DNA sequencing, from early methods like Maxam-Gilbert sequencing and Sanger sequencing, to newer technologies like 454 sequencing, Illumina sequencing, and Ion Torrent sequencing. These NGS methods allow for massively parallel sequencing of many DNA fragments to generate millions of short reads. The presentation outlines the types of NGS instruments and their applications in fields like molecular biology, medicine, and forensics. It also discusses future challenges in DNA sequencing and decreasing costs to analyze more human genomes.
Next generation-sequencing.ppt-convertedShweta Tiwari
The advance version, sequences the whole genome efficiently with high speed and high throughput sequencing at reduce cost is termed as Next Generation Sequencing (NGS) or massively parallel sequencing (MPS).
Next Generation Sequencing (NGS) Is A Modern And Cost Effective Sequencing Technology Which Enables Scientists To Sequence Nucleic Acids At Much Faster Rate. In This Presentation, You Will Learn About What is NGS, Idea Behind NGS, Methodology And Protocol, Widely Adapted NGS Protocols, Applications And References For Further Study.
A full picture of -omics cellular networks of regulation brings researchers closer to a realistic and reliable understanding of complex conditions. For more information, please visit: http://tbioinfopb.pine-biotech.com/
White Paper: Next-Generation Genome Sequencing Using EMC Isilon Scale-Out NAS...EMC
This EMC Isilon sizing and performance guideline White Paper reviews the Key Performance Indicators (KPIs) that most strongly impact the production processes for the storage of data from Next-Generation Sequencing (NGS) workflows.
The SOLiD 3 System provides high throughput DNA sequencing with several advantages over other technologies:
- It can sequence entire transcriptomes without any gaps, determine strand-specific expression patterns, and detect SNPs with low false positives.
- Applications include assessing DNA-protein interactions across multiple samples, discovering novel transcripts and splice variants without microarray bias, and characterizing structural rearrangements.
- The system uses emulsion PCR to clonally amplify template beads, followed by deposition of modified beads on a flow cell and sequencing by ligation using fluorescently labeled di-base probes.
Next-generation sequencing course, part 1: technologiesJan Aerts
This document provides an overview of next-generation sequencing technologies and their applications. It discusses genome enrichment techniques to isolate targeted regions for sequencing. It also describes template preparation methods like emulsion PCR and solid-phase amplification. Finally, it reviews various sequencing platforms like Illumina, SOLiD, 454 and details the sequencing and imaging processes. There are exercises proposed to work with sequencing data files in Galaxy.
RNASeq - Analysis Pipeline for Differential ExpressionJatinder Singh
RNA-Seq is a technique that uses next generation sequencing to sequence RNA transcripts and quantify gene expression levels. It can be used to estimate transcript abundance, detect alternative splicing, and compare gene expression profiles between healthy and diseased tissue. Computational challenges include read mapping due to exon-exon junctions and normalization of read counts. Key steps in RNA-Seq analysis include read mapping, transcript assembly, counting and normalizing reads, and detecting differentially expressed genes.
CSU Next Generation Sequencing Core 06/09/2015Richard Casey
The Next Generation Sequencing Core at Colorado State University provides next generation sequencing and bioinformatics services and support using Illumina and Ion Torrent sequencing platforms for applications such as DNA sequencing, RNA sequencing, epigenetics, metagenomics, and more, drawing on over 10 years of experience and resources including on-campus laboratories, computational infrastructure, and staff expertise. Services include laboratory preparation, sequencing runs, bioinformatics analysis, and training.
This document discusses computational methods and challenges for genome assembly using next-generation sequencing data. It describes the four main stages of genome assembly as preprocessing filtering, graph construction, graph simplification, and postprocessing filtering. Each stage processes the data from the previous stage to build the assembly graph and reduce complexity, though some assemblers delay filtering steps.
This document provides an overview of DNA microarrays (DNA chips), including:
1. It describes how DNA microarrays work, the basic components and steps involved including manufacturing probes, sample preparation, hybridization, scanning, and data analysis.
2. It discusses the two main types of microarrays - cDNA microarrays produced by robotic spotting and oligonucleotide arrays produced by in situ synthesis.
3. It outlines some of the applications of DNA microarrays including analyzing gene expression, disease classification, toxicogenomics, and more.
Slide Deck from Josh's 2014 presentation at the Illumina user group meeting in RTP. Slides describe our experience with V3 and V4 chemistries on a very large cohort of exome sequenced samples.
The document discusses DNA microarrays, including their applications, history, major steps, methods of construction, and technical issues. DNA microarrays allow analysis of gene expression across thousands of genes simultaneously. They have been used since the 1990s and are constructed by attaching DNA probes to a solid surface in a high-density array. Two main types are cDNA-based microarrays using amplified cDNA and oligonucleotide-based arrays like Affymetrix GeneChips containing short DNA sequences.
The document provides information about a presentation on bioinformatics and DNA sequencing. It includes 5 sections written by different group members. The summary is:
The presentation discusses DNA sequencing methods including Sanger sequencing. It describes the DNA sequencing process which involves separating newly synthesized DNA strands by length using heating and loading them into a capillary tube, passing the strands through a laser beam to cause dye fluorescence detected by a photocell, and computers interpreting the color sequence. Modern applications of sequencing include forensics, medicine, and agriculture.
Nanopore sequencing is a technique that determines DNA sequences by passing DNA fragments through a protein pore. It has the advantages of a small sequencer size, long read lengths, and potential for direct RNA sequencing. However, the raw nanopore data is complex and requires processing to transform it into usable genomic sequence information. The document discusses the nanopore sequencing technology, characteristics of the raw data, steps to process the raw data into a training dataset to predict genomic bases, and future directions for the technology.
DNA sequencing determines the order of nucleotides in a DNA segment. The first generation methods developed in 1977 were Maxam-Gilbert and Sanger sequencing, with Sanger becoming the most common. Next generation sequencing now includes Illumina, which is the most widely used, as well as PacBio and Nanopore third generation real-time single molecule techniques.
The document summarizes the work of the Genome in a Bottle Consortium to develop reference materials for benchmarking human structural variant calls. The Consortium has characterized structural variants over 50 base pairs in size across five human genomes using multiple long-read and linked-read sequencing technologies. The characterized variants are released as benchmark sets to evaluate the accuracy of different sequencing technologies in detecting structural variants. Ongoing work includes improving benchmarks for complex variants and collaborating to characterize more difficult genomic regions.
Gene sequencing is the technique that determines the order of nucleotide bases in DNA. It allows researchers to read genetic information and understand genes. The first genome sequenced was a bacteriophage in 1977. Major advances include sequencing the human genome in 2001. Current technologies like Illumina and Ion Torrent can generate billions of reads faster and cheaper than Sanger sequencing. Gene sequencing has applications in medicine, forensics, agriculture, and more. It is an important tool for understanding genomes and their relationship to traits and disease.
Gene sequencing is the technique that determines the order of nucleotide bases in DNA. It allows researchers to read genetic information and understand genes. The first genome sequenced was a bacteriophage in 1977. Techniques have advanced from Sanger sequencing to second-generation sequencing using platforms like Illumina and third-generation single-molecule techniques. Gene sequencing has various applications in medicine, forensics, agriculture, cancer research and more. It is an important tool for understanding genomes and their relationship to traits and disease.
The Genome in a Bottle Consortium held a workshop in August 2014 at NIST to discuss progress and plans.
- They have developed a pilot reference material (RM) using the genome of individual NA12878, releasing 8,300 vials to participants for sequencing and analysis.
- They are working to characterize additional genomes from the Personal Genome Project, including an Ashkenazi Jewish trio and their Asian son, to serve as future reference materials.
- At the workshop they discussed expanding the types of variants characterized in reference materials, selecting future genomes, and obtaining necessary approvals to release human genomes as reference materials.
This document discusses the history and evolution of DNA sequencing technologies. It begins with early manual sequencing methods developed in the 1970s by Sanger and others. Automated Sanger sequencing and the sequencing of larger genomes followed in the 1980s-1990s. Next generation sequencing (NGS) methods were developed starting in 1996 and became commercially available in 2005, enabling massively parallel sequencing. NGS platforms such as 454, Illumina, and SOLiD are discussed. Third generation real-time sequencing methods such as PacBio and nanopore sequencing are also introduced, providing longer read lengths. The document compares key parameters of different sequencing methods such as read length, accuracy, throughput, cost and advantages/disadvantages.
Generations of sequencing technologies. ShadenAlharbi
This document discusses the history and evolution of DNA sequencing technologies. It describes 3 generations of sequencing: 1) First generation sequencing involved Sanger chain termination sequencing; 2) Second generation sequencing included 454 pyrosequencing, Illumina sequencing, and SOLiD sequencing, which allowed massively parallel sequencing; 3) Third generation sequencing features long read lengths up to 50,000 bp from technologies like nanopore sequencing from Oxford Nanopore and single molecule real-time sequencing. The document provides details on the workflow and chemistry of various sequencing platforms.
Text Independent Speaker recognitom framework for detecting criminals.pptGrace136708
The document describes a proposed text-independent speaker recognition system to detect criminals. It discusses motivations like security issues in developing countries and limitations of existing systems. The objectives are to identify weaknesses in current approaches and develop an improved system for efficient criminal detection. It outlines the methodology, which involves combining autoassociative neural networks and vector quantization for classification after MMFCC feature extraction. Implementation details and initial results demonstrating the system matching test speakers to trained clusters are also provided.
The Genome in a Bottle Consortium is developing reference materials, reference methods, and reference data to assess confidence in human whole genome variant calls. The Consortium is characterizing several human genomes including the NA12878 genome, an Ashkenazi Jewish trio, and a Chinese trio from the Personal Genome Project. Data generated for these genomes includes various sequencing technologies from Illumina, Complete Genomics, PacBio, BioNano, and others. The Consortium is developing high-confidence variant calls for SNPs, indels, structural variants, and phasing. Individual datasets and integrated variant calls will be made publicly available on the GIAB FTP site.
This document summarizes a student's placement experience at Source Bioscience, a company that provides genomic services including DNA sequencing, microarray analysis, and testing for STIs.
The student's role was as a Trainee DNA Sequencing Scientist, where they prepared and sequenced DNA samples using Sanger sequencing. Sanger sequencing involves making copies of a DNA region using DNA polymerase, primers, nucleotides, and chain terminators to determine the base pair sequence.
The student gained experience with accurate pipetting, meeting turnaround times, customer contact, data interpretation, and teamwork. They provided examples of sequencing runs that were successful and unsuccessful. In conclusion, the student thanks the listener and offers to answer any questions about
The Genome-in-a-Bottle Consortium was established to develop reference materials for clinical applications of human genome sequencing. The National Institute of Standards and Technology (NIST) has been working with various organizations to obtain and characterize reference genomes. The current plan is to use the NA12878 genome as a pilot sample and 8 trios from the Personal Genome Project as a more complete set. Working groups were formed to address reference material selection, characterization measurements, bioinformatics/data integration, and performance metrics. The consortium discussed obtaining consent for reference genomes, the scope of work, and how decisions will be made regarding new reference materials and policies.
Next-generation sequencing (NGS) has various applications in livestock genetics and breeding including:
1. Whole genome sequencing to identify genetic variations within and between species and quantify introgression.
2. RNA sequencing to detect differentially expressed genes between control and infected/challenged animals and identify genes related to disease resistance.
3. Genome-wide association studies using SNPs identified through NGS to map quantitative trait loci and guide marker-assisted selection for improved traits.
The document discusses various genomic and proteomic tools and techniques that have revolutionized the field of microbial physiology. The advent of personal computers, the Internet, and rapid DNA sequencing techniques has fueled this renaissance by enabling widespread sharing of information among scientists. Genomic tools like gene cloning and sequencing provide insights into complete genetic instructions, while proteomic techniques examine dynamic protein expression and interactions. A variety of methods are described, including two-dimensional gel electrophoresis, mass spectrometry, and gene arrays.
Open pacbiomodelorgpaper j_landolin_20150121Jane Landolin
Jane Ladolin's slides on Open Data Paper (http://www.nature.com/articles/sdata201445) presented at Balti and Bioinformatics virtual meeting on Jan. 21st 2015. (http://bit.ly/1KYGxr4)
The independent study on how Cloud Computing can be used to introduce a new Next Generation Sequencing method in terms of better understanding of the limitations of existing Next Generation Sequencing Methods.
Challenges in HIV prevention Tashfeen Ahmad.pptxTashfeen Ahmad
This document discusses challenges in preventing the spread of HIV/AIDS. It notes that while treatment has increased life expectancy for those with HIV, new infections still outpace treatments. Barriers to effective prevention strategies include lack of awareness of HIV status, fear of testing, inability to maintain ongoing treatment, and insufficient funding and resources for prevention programs. Overcoming these challenges requires greater implementation of prevention strategies, increasing awareness of HIV/AIDS, raising funds for treatment and testing centers, and improving access to preventive tools and care.
The pericardium is a fibro-serous sac that surrounds the heart and restricts its movement. It has two layers - an outer fibrous layer that maintains the heart's position and an inner serous layer with parietal and visceral layers separated by pericardial fluid. The pericardium protects the heart and provides lubrication as the heart beats within its sac. It has reflections around the major blood vessels leaving the heart and contains openings that allow for blood vessel passage.
Challenges in HIV prevention were presented by a medical student. Some key challenges discussed include failure to implement prevention strategies effectively, with diagnosis, treatment coverage, and viral suppression varying widely between countries. Additional challenges include lack of awareness of HIV status, fear of testing, inability to maintain ongoing treatment, socioeconomic factors like poverty and lack of access to healthcare, unsafe sex practices, and inadequate resources for prevention. The conclusion calls for a focus on improved implementation of prevention strategies, increasing awareness, funding for treatment and prevention programs, and expanding access to preventive tools and services.
In the field of psychology, cognitive dissonance is the perception of contradictory information. Relevant items of information include a person's actions, feelings, ideas, beliefs, values, and things in the environment.
The document discusses pharmacology and drug metabolism, outlining the four stages of drug metabolism as absorption, transportation, biotransformation, and excretion. It also covers factors that affect drug metabolism and different routes of drug administration, with a focus on oral drug administration and the nursing process for safely administering oral medications.
Yellow fever is an acute viral disease transmitted by infected mosquitoes. It is caused by the yellow fever virus and primarily spreads through the bites of infected Aedes aegypti mosquitoes. The disease was originally found in Africa and was spread to the Americas via the slave trade. Symptoms include fever, chills, nausea and jaundice in some cases. There is no specific treatment, but supportive care can improve outcomes. Vaccination is the most important prevention method against yellow fever.
The document provides a single name, Tashfeen Ahmad, with an identifier of GM-4. No other context or details are given about this person. The very brief document only lists a name and identifier without any explanation of who this person is or what relevance the identifier has.
TEST BANK For Community Health Nursing A Canadian Perspective, 5th Edition by...Donc Test
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Cell Therapy Expansion and Challenges in Autoimmune DiseaseHealth Advances
There is increasing confidence that cell therapies will soon play a role in the treatment of autoimmune disorders, but the extent of this impact remains to be seen. Early readouts on autologous CAR-Ts in lupus are encouraging, but manufacturing and cost limitations are likely to restrict access to highly refractory patients. Allogeneic CAR-Ts have the potential to broaden access to earlier lines of treatment due to their inherent cost benefits, however they will need to demonstrate comparable or improved efficacy to established modalities.
In addition to infrastructure and capacity constraints, CAR-Ts face a very different risk-benefit dynamic in autoimmune compared to oncology, highlighting the need for tolerable therapies with low adverse event risk. CAR-NK and Treg-based therapies are also being developed in certain autoimmune disorders and may demonstrate favorable safety profiles. Several novel non-cell therapies such as bispecific antibodies, nanobodies, and RNAi drugs, may also offer future alternative competitive solutions with variable value propositions.
Widespread adoption of cell therapies will not only require strong efficacy and safety data, but also adapted pricing and access strategies. At oncology-based price points, CAR-Ts are unlikely to achieve broad market access in autoimmune disorders, with eligible patient populations that are potentially orders of magnitude greater than the number of currently addressable cancer patients. Developers have made strides towards reducing cell therapy COGS while improving manufacturing efficiency, but payors will inevitably restrict access until more sustainable pricing is achieved.
Despite these headwinds, industry leaders and investors remain confident that cell therapies are poised to address significant unmet need in patients suffering from autoimmune disorders. However, the extent of this impact on the treatment landscape remains to be seen, as the industry rapidly approaches an inflection point.
These lecture slides, by Dr Sidra Arshad, offer a quick overview of the physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar lead (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
6. Describe the flow of current around the heart during the cardiac cycle
7. Discuss the placement and polarity of the leads of electrocardiograph
8. Describe the normal electrocardiograms recorded from the limb leads and explain the physiological basis of the different records that are obtained
9. Define mean electrical vector (axis) of the heart and give the normal range
10. Define the mean QRS vector
11. Describe the axes of leads (hexagonal reference system)
12. Comprehend the vectorial analysis of the normal ECG
13. Determine the mean electrical axis of the ventricular QRS and appreciate the mean axis deviation
14. Explain the concepts of current of injury, J point, and their significance
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
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5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. Chapter 3, Cardiology Explained, https://www.ncbi.nlm.nih.gov/books/NBK2214/
7. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
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1. S
ADAM University of Kyrgyz Republic.
Faculty of medicine
Nanopore Sequencing
Student: Tashfeen Ahmad
Group:GM_4
Teacher: Prof. Domashov Iliya
2. Nanopore Sequencing
Outline
• Nanopore Sequencing Technology
• Raw Data
• Transformations and Raw Data Processing
• Toward Producing a Basecaller
• Future Directions
4. What is Nanopore
Sequencing?
Oxford Nanopore became the
first company to provide a
commercially available
nanopore sequencer in 2015
(available to community in
2012)
5. What is Nanopore
Sequencing?
Nanopore is a disruptive technology:
• Sequencer Size
• Read Length
• Potential direct RNA sequencing
• Biology Problem with Data Velocity Issues
• Currently ~400GB/24 hours needs to
be processed
8. Processing Raw Data
• First step is to create a training data set
• Starting from provided raw data followed by processing to produce useful
data set for training to predict genomic bases
• Goal is to release this package to the community for greater access to create
training data sets for this data
14. Nanopore Raw Correction
1. Center on
insertion
2. Expand to
neighboring
regions
3. Segment using
mean changepoint
Correct
insertions
:
CCC
CCCC
C
CG
G
G
GG
GGG
G
GG
G
GG
GGG
G
GGG
GG
G
G
G
GGG
GGGG
G
G
G
GGGG
GG
G
G
G
GGG
G
G
G
G
G
G
GG
G
G
G
G
G
GGGG
G
G
G
C
CC
CCCCCCCCCC
CCCCC
C
C
CCCCCCC
C
CCCCCCCCC
CCCCCC
CC
A
AAAAAAA
A
AG
GGGGGGG
G
GGGG
CCCCC
C
CCCCCCCCCCCCCCCCCCCCCC
CCCC
CCCC
CCCCCCCCCCCC
C
CCCCCC
CCCCCCCC
CTT
T
T
TTTTTTTTT
T
TT
TTT
TTTTTTTT
TTT
TTT
TTTT
TTT
T
TTTTT
T
TTTTTTTTTTT
TT
TTTTTTT
TTTTTTTT
TT
T
T
TTT
TTTTT
TTTTTTTT
T
T
GGGGGG
GGGGGGGGGG
GGGGGGGG
G
GG
GG
G
G
GGGGG
GGGG
GGGGGGGGGG
G
GG
GG
G
GGGG
G
GGGGG
G
GGGGGG
GG
G
G
G
G
GG
GGGGGG
GGGG
G
GGGGGGGGGGGG
G
G
GGG
G
G
GGGG
G
GG
GGGGGGGGGGGGGGGG
G
GGGG
GGGGGG
GGGGGGGGGGGGGGGGGG
GGG
GGGGG
G
G
GG
GGGGG
G
G
G
GGGGGGGGGGGG
GGGGGGGGGGGGGGGG
G
GGGGGGGGGG
GGGGGGGGGGG
GG
G
GG
GGGG
G
GGG
G
GGGGGGGGGGG
G
G
GGGGG
GGGGGGGGGGG
GGGGGGGGG
GG
GGGGG
GGGGGG
GGG
GGGGG
GGGG
GGGGG
G
GGGGG
GGGGGGGGG
GGGGGGGGGG
GGGG
GG
GGG
GG
GGGGGGGGGGG
G
GG
GG
G
GG
GG
G
GG
GGGG
GGG
GG
GG
GGGGGGGGG
G
G
G
GGGGGGGGG
G
GG
G
G
G
GG
G
G
G
G
GG
GGGGGG
G
GG
GGG
G
G
GG
G
GG
GG
G
GG
G
G
GGG
G
G
GG
C
CCCCCC
CCCCCCC
C
A
AAA
AAAA
AAA
AA
AAA
A
T
TTTTTTTTTTTTTTT
TTTT
T
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTT
AAAA
AAAAAAAAAAAA
AAAAAAAAAAAAAAA
CCCCC
C
CCC
CCCCCCCCCCC
CCCCCCC
CCC
CCCCCCCCCCC
CC
CCCTTTTTTTTT
TTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTT
TT
T
G
GGGGGG
GGGG
DDDDDDDDDD
DDDDDDD
DDDD
D
DDDD
DD
D
DD
D
D
G
GG
GGGG
GG
GG
CC
C
CC
CCCCCC
CCCC
CCCC
A
A
AA
A
A
A
A
A
AA
A
A
AA
A
A
A
A
A
AA
AAAA
A
A
AAA
AAA
A
AA
A
AA
AA
AA
AA
A
AA
A
A
A
AAAA
A
A
AAAAAAAAAA
CCCCC
CCCCCCCC
C
C
C
CCCCCCC
C
C
CCCCCCC
CCCCCC
C
CCC
CC
C
CCCC
GGGGGGG
T
6523000 4652400
CCC
C
C
CG
G
G
GGGGG
G
GG
G
GGGGGGGGG
GG
GG
G
GGGGGGG
GGG
GGGG
GG
G
G
G
GGG
G
G
G
G
G
GGG
GG
G
G
G
GGGGGG
G
C
CC
CCC
CCCCCCC
CCCCC
C
C
CCCCCCC
C
CCCCCCCCC
CCCCCC
CC
A
AAAAAAA
A
AG
GGGGGGG
G
GGGG
CCCCC
C
CCCCCCCCCCCC
CCCCCCCCC
C
C
CCC
CCCC
CCCCCCCCCCCC
C
CCC
CCC
CCCCCCCC
C
TTT
T
TTTTTTTTTT
TTTTT
TTTTTTTT
TTT
TTT
TTTTTTT
T
TTTTT
TTTTTTTTTTTT
TT
TTTTTTTTTTTTTTTTTT
T
TTT
TTTTT
TTTTTTTT
T
T
GGGGG
G
GGGGGGGGG
G
GGGGG
G
GG
G
GG
GG
G
G
GGGG
G
GGGG
GGGGGGGGG
G
G
G
G
GG
G
GGGG
G
GGGGG
G
GGGGGG
GG
G
G
G
G
GG
GGGGGG
TTTT
T
TTTTTTTTTTTT
T
T
TTT
T
T
GGGG
G
GG
GGGGGGGGGGGGGGGG
G
GGGG
GGGGGG
GGGGGGGGGGGGGGGGGG
GGG
GGGGG
G
G
GG
GGGGG
G
G
G
GGGGGGGGGGGG
GGGGGGGGGGGGGGGG
G
G
GGGGGGGGG
GGGGGGGGGGG
GG
G
GG
GGGG
G
GGG
G
GGGGGGGGGGG
G
G
GGGGG
GGGGGGGGGGG
GGGGGGGGG
GG
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GGGGGG
GGG
GGGGG
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GGGGG
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GGGGGGGGG
GGGGGGGGGG
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GG
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GG
G
GG
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GGG
G
G
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G
GG
G
G
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G
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C
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C
A
AAA
AAAA
AAA
AA
AAA
AT
TTTTTTT
TTTTTTT
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TTTTTTTTTT
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TTTTTTTT
TTTTTTTTTTTTTTTTTTT
TTTTTTTT
TT
T
TT
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AAAA
A
AAAA
AAAAAA
A
AAAAAAAAAAAAAAA
CCCCC
C
CCC
CCCCCCCCCCC
CCCCCCC
CCC
CC
C
CCCCCCC
C
CC
C
CCTTTTTTTT
T
TTTTTTTTTTT
TTTTTTTTT
T
TT
T
TTTT
TT
T
TTTTTTTT
T
TT
T
G
GGGGGG
GGGG
GGGGGGGGGG
GGGGGGG
GGGG
G
GGGG
GG
G
GG
G
G
G
GG
GGGGGG
GG
C
C
C
CC
CCCCCC
CCCC
CCCC
A
A
AA
A
A
AAAAA
A
A
AA
A
AAAAAAAAAAAA
AAA
AAA
A
AA
A
AA
AA
AA
AAA
AAA
A
A
AAAA
A
A
AAAAAAAAAA
CCCCCCCCCCCCCCC
C
CCCCCCC
CCCCCCCCCCCCCCCC
CCCCC
C
CCCC
GGGGGGG
6523000 4652400
CCC
CCCC
C
CG
G
G
GG
GGG
G
GG
G
GG
GGG
G
GGG
GG
G
G
G
GGG
GGGG
G
G
G
GGGG
GG
G
G
G
GGG
G
G
G
G
G
G
GG
G
G
G
G
G
GGGG
G
G
G
C
CC
CCCCCCCCCC
CCCCC
C
C
CCCCCCC
C
CCCCCCCCC
CCCCCC
CC
A
AAAAAAA
A
AG
GGGGGGG
G
GGGG
CCCCC
C
CCCCCCCCCCCCCCCCCCCCCC
CCCC
CCCC
CCCCCCCCCCCC
C
CCCCCC
CCCCCCCC
CTT
T
T
TTTTTTTTT
T
TT
TTT
TTTTTTTT
TTT
TTT
TTTT
TTT
T
TTTTT
T
TTTTTTTTTTT
TT
TTTTTTT
TTTTTTTT
TT
T
T
TTT
TTTTT
TTTTTTTT
T
T
GGGGGG
GGGGGGGGGG
GGGGGGGG
G
GG
GG
G
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GGGGG
GGGG
GGGGGGGGGG
G
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G
GGGGGG
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GGGG
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GGGG
G
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GGGGGGGGGGGGGGGG
G
GGGG
GGGGGG
GGGGGGGGGGGGGGGGGG
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GGGGG
G
G
GG
GGGGG
G
G
G
GGGGGGGGGGGG
GGGGGGGGGGGGGGGG
G
G
GGGGGGGGG
GGGGGGGGGGG
GG
G
GG
GGGG
G
GGG
G
GGGGGGGGGGG
G
G
GGGGG
GGGGGGGGGGG
GGGGGGGGG
GG
GGGGG
GGGGGG
GGG
GGGGG
GGGG
GGGGG
G
GGGGG
GGGGGGGGG
GGGGGGGGGG
GGGG
GG
GGG
GG
GGGGGGGGGGG
G
GG
GG
G
GG
GG
G
GG
GGGG
GGG
GG
GG
GGGGGGGGG
G
G
G
GGGGGGGGG
G
GG
G
G
G
GG
G
G
G
G
GG
GGGGGG
G
GG
GGG
G
G
GG
G
GG
GG
G
GG
G
G
GGG
G
G
GG
C
CCCCCC
CCCCCCC
C
A
AAA
AAAA
AAA
AA
AAA
A
T
TTTTTTTTTTTTTTT
TTTT
T
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTT
AAAA
AAAAAAAAAAAA
AAAAAAAAAAAAAAA
CCCCC
C
CCC
CCCCCCCCCCC
CCCCCCC
CCC
CCCCCCCCCCC
CC
CCCTTTTTTTTT
TTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTT
TT
T
G
GGGGGG
GGGG
DDDDDDDDDD
DDDDDDD
DDDD
D
DDDD
DD
D
DD
D
D
G
GG
GGGG
GG
GG
CC
C
CC
CCCCCC
CCCC
CCCC
A
A
AA
A
A
A
A
A
AA
A
A
AA
A
A
A
A
A
AA
AAAA
A
A
AAA
AAA
A
AA
A
AA
AA
AA
AA
A
AA
A
A
A
AAAA
A
A
AAAAAAAAAA
CCCCC
CCCCCCCC
C
C
C
CCCCCCC
C
C
CCCCCCC
CCCCCC
C
CCC
CC
C
CCCC
GGGGGGG
T
6523000 4652400
CCC
C
C
CG
G
G
GGGGG
G
GG
G
GGGGGGGGG
GG
GG
G
GGGGGGG
GGG
GGGG
GG
G
G
G
GGG
G
G
G
G
G
GGG
GG
G
G
G
GGGGGG
G
C
CC
CCC
CCCCCCC
CCCCC
C
C
CCCCCCC
C
CCCCCCCCC
CCCCCC
CC
A
AAAAAAA
A
AG
GGGGGGG
G
GGGG
CCCCC
C
CCCCCCCCCCCC
CCCCCCCCC
C
C
CCC
CCCC
CCCCCCCCCCCC
C
CCC
CCC
CCCCCCCC
C
TTT
T
TTTTTTTTTT
TTTTT
TTTTTTTT
TTT
TTT
TTTTTTT
T
TTTTT
TTTTTTTTTTTT
TT
TTTTTTTTTTTTTTTTTT
T
TTT
TTTTT
TTTTTTTT
T
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GGGGG
G
GGGGGGGGG
G
GGGGG
G
GG
G
GG
GG
G
G
GGGG
G
GGGG
GGGGGGGGG
G
G
G
G
GG
G
GGGG
G
GGGGG
G
GGGGGG
GG
G
G
G
G
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GGGGGG
TTTT
T
TTTTTTTTTTTT
T
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TTT
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GGGG
G
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GGGGGGGGGGGGGGGG
G
GGGG
GGGGGG
GGGGGGGGGGGGGGGGGG
GGG
GGGGG
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C
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GGGGGG
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6523000 4652400
16. Raw Nanopore Data
• Noise level is quite high (hopeful for improvements in base technology)
• Shown above is the same DNA sequence observed 8 times
17. Toward a Basecaller
Post correction and
normalization distributions
• Clearly some signal exists
before complex machine
learning
• ~13% accuracy achievable by
nearest mean calculations
18. Toward a Basecaller
• Oxford Nanopore has recently upgraded to a RNN basecaller which
produces reads with ~85% accuracy, thought it is still computationally
intensive
• Larger sequencer (PromethION) produces 12Tb of data in 48 hours (up to
1.44GBps) with current machine requiring ~1kW.
19. Toward a Basecaller
Current event (base) segmentation is
done using an FPGA t-test and all
computation (RNN) is completed on
the mean and SD of these segments
We are currently working to integrate
basecalling and segmentation directly
from the raw data via an RNN with
potentially vast improvements in
accuracy as well as speed which will
become increasingly important with
throughput improvements. 0.00
0.25
0.50
0.75
1.00
0.00 0.25 0.50 0.75 1.00
FPRate
TPRate
−2
−1
0
1
log10FDR
20. Challenges
• Data Velocity
• Basecaller must be able to keep up with the increasing speed of the data
• Accuracy
• Basecaller must be accurate enough to provide meaningful biological
insight
• Adaptabiltiy
• Would like to be able to interrogate the data in order to assess confidence
as well as possible alterations outside of the given model
21. Future Directions
• Produce 1D basecalls on par with current algorithms ~70-80%
• Exploring architectures and pre-processing
• Investigate base alterations (methylation, acetylation, etc.) via encoding layers
• Release package to create raw data training sets and provide QC metrics for
raw reads.