Developing Reliable QC at the Swedish National Genomics Infrastructure
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Good quality control procedures are essential for sequencing facilities. The SciLifeLab National Genomics Infrastructure is an accredited facility that processes thousands of samples every month, driving us to develop high-throughput QC procedures. We use a LIMS, a bespoke web system and most recently MultiQC - a tool that I have written to summarise analysis log files and produce reports that visualise key sample metrics. In this talk I describe how our different systems integrate and how we use MultiQC results for both project level reporting and long term monitoring.
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The future of genomics in the cloud
Slides from my talk given at the AWS Loft event in Stockholm, November 2018.
When genomic data is staged for analysis on Amazon S3, researchers have fast access to large volumes of data without needing to download and store their own copies. In this session, you will learn how a researcher at Sweden's SciLifeLab has made reference genome data available in the cloud as an AWS Public Dataset, and how this makes it easier for researchers to do large scale genomic analysis using tools like EMR and AWS Batch.
SciLifeLab NGI NovaSeq seminar
Talk from the SciLifeLab NGI NovaSeq seminar in September 2018. I describe how differences in illumina sequencing on the new NovaSeq 6000 can affect your sequencing, with illustrated examples from qcfail.com
SBW 2016: MultiQC Workshop
This document discusses NGS quality control using MultiQC. It provides background on the large volume of sequencing data processed in 2016 at NGI Stockholm, including different sequencing types and the challenges of manual quality control. It then introduces MultiQC as a tool that parses key metrics from analysis results/logs to create a single HTML report summarizing a project. It provides information on how MultiQC works, how to install and run it, and exercises for users. It also discusses customizing MultiQC reports and developing new modules.
NBIS ChIP-seq course
Slides from my talk as part of the NBIS ChIP-seq tutorial course. I describe how we process ChIP-seq data at the Swedish National Genomics Infrastructure and how our NGI-ChIPseq analysis pipeline works. https://github.com/SciLifeLab/NGI-ChIPseq
NBIS RNA-seq course
Slides from my talk as part of the NBIS RNA-seq tutorial course. I describe how we process RNA-seq data at the Swedish National Genomics Infrastructure and how our NGI-RNAseq analysis pipeline works. https://github.com/SciLifeLab/NGI-RNAseq
Using visual aids effectively
Using effective visual aids is important for getting across your message when describing data. This can be in a presentation, poster or paper. This talk goes through some basic design tips that can help your visual aids look professional and work effectively.
Written for the Enabling Excellence ETN. https://eetraining.wordpress.com/
Analysis of ChIP-Seq Data
This document discusses the bioinformatics analysis of ChIP-seq data. It begins with an overview of ChIP-seq experiments and the major steps in processing and analyzing the sequencing data, including quality control, alignment, peak calling, and downstream analyses. Pipelines for automated analysis are described, such as Cluster Flow and Nextflow. The talk emphasizes that there is no single correct approach and the analysis depends on the biological question and experimental design.
Internet McMenemy
The document discusses how the internet and websites work from a technical perspective. It covers how a web address is resolved to a server, the basic components of a webpage like HTML, CSS and images, how databases and templates allow dynamic content, and how cookies are used to store information on a user's browser. Real examples of code are provided to illustrate these concepts. Useful links are also included for hosting and creating websites.
More from Phil Ewels (14)
Reproducible bioinformatics for everyone: Nextflow & nf-core
Reproducible bioinformatics for everyone: Nextflow & nf-core
Reproducible bioinformatics workflows with Nextflow and nf-core
Reproducible bioinformatics workflows with Nextflow and nf-core
ELIXIR Proteomics Community - Connection with nf-core
ELIXIR Proteomics Community - Connection with nf-core
Nextflow Camp 2019: nf-core tutorial (Updated Feb 2020)
Nextflow Camp 2019: nf-core tutorial (Updated Feb 2020)
Recently uploaded
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
原版纸张【微信：741003700 】【(uvic毕业证书)维多利亚大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
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如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
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◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
ESR spectroscopy in liquid food and beverages.pptx
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...Abdul Wali Khan University Mardan,kP,Pakistan
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skillsTravis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Recently uploaded (20)
Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
8.Isolation of pure cultures and preservation of cultures.pdf
8.Isolation of pure cultures and preservation of cultures.pdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
aziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobel
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Cytokines and their role in immune regulation.pptx
Cytokines and their role in immune regulation.pptx
bordetella pertussis.................................ppt
bordetella pertussis.................................ppt
ESR spectroscopy in liquid food and beverages.pptx
ESR spectroscopy in liquid food and beverages.pptx
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Developing Reliable QC at the Swedish National Genomics Infrastructure
- 1. High Throughput QC Quality Control at the Swedish National Genomics Infrastructure Phil Ewels @ewels @tallphil Bioinfo-Core Workshop 2017-07-24 ISMB 2017, Prague
- 2. ISO accredited facility Library preparation Sequencing Bioinfo analysis NGI stockholm
- 3. ISO accredited facility Library preparation Sequencing Bioinfo analysis “This means that our services are subject to highly stringent quality control procedures, so that you can be sure that your data is of excellent quality.” NGI stockholm
- 4. 2 x MiSeq 5 x HiSeq 2500 5 x HiSeq X10 NovaSeq RNA-Seq WG Re-Seq Targeted Re-Seq Metagenomics Others 0 2000 4000 6000 8000 10000 12000 14000 1,265 2,580 3,214 8,934 12,017 Number of Samples in 2016 1141 Gbp/day 1X Human Genome every 4 minutes NGI stockholm
- 5. QC with lots of samples Always Occasionally Automation Visualisation (spot outliers) Manual checks Validations Looking for trends Good quality control at scale is essential
- 6. QC Automation All sample metadata in a database Genomics Status OrderPortal
- 8. QC Automation Collection + visualisation of results
- 9. QC Automation Collection + visualisation of results Genomics Status
- 10. Genomics Status
- 15. QC with lots of samples Always Occasionally Automation Visualisation (spot outliers) Manual checks Validations Looking for trends
- 16. Long term trends coming soon…
- 17. Long term trends Data available from 2253 samples, 738 reports Choose a plot type1 Select data2 Data HistogramReport plot Compare DataData Trend
- 18. Long term trends Data available from 2253 samples, 738 reports Select samples2 Choose a plot type1 Data Trend + Add Filter Metadata field: [ select value ] Minimum: Maximum [ 837 samples ] Date: 2017.01.01 - 2017.03.01 Application Type: WGS
- 19. Long term trends Data available from 2253 samples, 738 reports Select samples2 Choose a plot type1 Data Trend [ 837 samples ] Plot data3 Picard: % Dups Qualimap: > 30X [ add data ]
- 20. • Each lab technique has a protocol • Changes require validation • Internal audits • Horizontal (one step) • Vertical (one sample) NGI stockholm Validations In-depth reproducibility checks stockholm uppsala NGI stockholm
- 21. Analysis Validation • Versioned pipeline releases • New versions require a validation test • Runs logged and reported • Continuous integration tests
- 24. Conclusion http://github.com/SciLifeLab http://multiqc.info http://opensource.scilifelab.se NGI stockholm Phil Ewels phil.ewels@scilifelab.se ewels tallphil Acknowledgements Max Käller Rickard Hammarén Denis Moreno Francesco Vezzi NGI Stockholm Genomics Applications Development Group