Variant Analysis

Jekyll 2026-01-21T17:14:51+00:00 https://training.galaxyproject.org/training-material/topics/variant-analysis/feed.xml Variant Analysis Recently added tutorials, slides, FAQs, and events in the variant-analysis topic https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png 📅 Galaxy Training Academy 2026 https://training.galaxyproject.org/training-material/events/2026-05-18-galaxy-academy.html 2026-01-21T17:14:51+00:00

The Galaxy Training Academy is a self-paced online training event for beginners and advanced learners who want to improve their data analysis skills in Galaxy and/or in popular fields in bioinformatics. Over the course of one week, we offer a diverse selection of learning tracks for you.

Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ 📅 Workshop on high-throughput sequencing data analysis with Galaxy https://training.galaxyproject.org/training-material/events/2026-03-09-hts-workshop-freiburg.html 2025-10-23T19:56:37+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is designed for beginners; no prior programming skills are required.

Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ 🎥 Recording of Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/recordings/#tutorial-recording-8-may-2025 2025-05-08T00:00:00+00:00

A 31M long recording is now available.

Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ 🛠️ Workflow to detect SNV from Illumina sequenced baculovirus isolates https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/baculovirus-isolate-variation/workflows/Workflow-to-detect-SNV-from-Illumina-sequenced-baculovirus-isolates.html 2025-02-24T15:19:25+00:00

This standard workflow determines SNV positions from baculovirus isolates using bcftools.

Jörg T. Wennmann 📚 Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html 2025-02-24T15:19:25+00:00

Baculoviruses of the family Baculoviridae (Harrison et al. 2018) are among the most intensively

Jörg Wennmann https://training.galaxyproject.org/training-material/hall-of-fame/wennj/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Jörg Wennmann https://training.galaxyproject.org/training-material/hall-of-fame/wennj/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📅 Galaxy Training Academy 2025 https://training.galaxyproject.org/training-material/events/2025-05-12-galaxy-academy-2025.html 2025-02-10T19:40:45+00:00

The Galaxy Training Academy is a self-paced online training event for beginners and advanced learners who want to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track for you.

Delphine Lariviere https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Scott Cain https://training.galaxyproject.org/training-material/hall-of-fame/scottcain/ Natalie Whitaker-Allen https://training.galaxyproject.org/training-material/hall-of-fame/natalie-wa/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Armin Dadras https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ Ahmed Hamid Awan https://training.galaxyproject.org/training-material/hall-of-fame/ahmedhamidawan/ Anna Syme https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/ Anne Fouilloux https://training.galaxyproject.org/training-material/hall-of-fame/annefou/ Anup Kumar https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Dannon Baker https://training.galaxyproject.org/training-material/hall-of-fame/dannon/ Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ Elifsu Filiz https://training.galaxyproject.org/training-material/hall-of-fame/elifsu-simula/ Eli Chadwick https://training.galaxyproject.org/training-material/hall-of-fame/elichad/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Emmanuel Augustine https://training.galaxyproject.org/training-material/hall-of-fame/emmaustin20/ Even Moa Myklebust https://training.galaxyproject.org/training-material/hall-of-fame/evenmm/ Gareth Price https://training.galaxyproject.org/training-material/hall-of-fame/GarethPrice-Aus/ Hans-Rudolf Hotz https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ Helena Vela https://training.galaxyproject.org/training-material/hall-of-fame/hvelab/ Igor Makunin https://training.galaxyproject.org/training-material/hall-of-fame/igormakunin/ Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ John Davis https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/ Jean Iaquinta https://training.galaxyproject.org/training-material/hall-of-fame/j34ni/ Jennifer Hillman-Jackson https://training.galaxyproject.org/training-material/hall-of-fame/jennaj/ Julian Hahnfeld https://training.galaxyproject.org/training-material/hall-of-fame/jhahnfeld/ Jochen Blom https://training.galaxyproject.org/training-material/hall-of-fame/jochenblom/ Lisanna Paladin https://training.galaxyproject.org/training-material/hall-of-fame/lisanna/ Linda Fenske https://training.galaxyproject.org/training-material/hall-of-fame/lfenske-93/ Matthias Bernt https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/ Max Pfister https://training.galaxyproject.org/training-material/hall-of-fame/PfisterMaxJLU/ Melanie Föll https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/ Meltem Kutnu https://training.galaxyproject.org/training-material/hall-of-fame/meltemktn/ Michael Schatz https://training.galaxyproject.org/training-material/hall-of-fame/mschatz/ Michelle Terese Savage https://training.galaxyproject.org/training-material/hall-of-fame/hujambo-dunia/ Eduardo Jacobo Miranda Ackerman https://training.galaxyproject.org/training-material/hall-of-fame/mirandaembl/ Nate Coraor https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/ Oliver Rupp https://training.galaxyproject.org/training-material/hall-of-fame/Oliver_Rupp/ Oliver Schwengers https://training.galaxyproject.org/training-material/hall-of-fame/oschwengers/ Paul De Geest https://training.galaxyproject.org/training-material/hall-of-fame/pauldg/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Polina Polunina https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ Krzysztof Poterlowicz https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/ Pratik Jagtap https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/ Rand Zoabi https://training.galaxyproject.org/training-material/hall-of-fame/RZ9082/ Romane LIBOUBAN https://training.galaxyproject.org/training-material/hall-of-fame/rlibouba/ Reyhaneh Tavakoli https://training.galaxyproject.org/training-material/hall-of-fame/reytakop/ Saim Momin https://training.galaxyproject.org/training-material/hall-of-fame/SaimMomin12/ Sanjay Kumar Srikakulam https://training.galaxyproject.org/training-material/hall-of-fame/sanjaysrikakulam/ Silvia Di Giorgio https://training.galaxyproject.org/training-material/hall-of-fame/silviadg87/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Subina Mehta https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ Timothy J. Griffin https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/ Tyler Collins https://training.galaxyproject.org/training-material/hall-of-fame/tcollins2011/ Wendi Bacon https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📅 Workshop on high-throughput sequencing data analysis with Galaxy https://training.galaxyproject.org/training-material/events/2025-03-10-hts-workshop-freiburg.html 2024-10-15T12:38:08+00:00

This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.

Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ 🎥 Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/recordings/#tutorial-recording-27-september-2024 2024-09-27T00:00:00+00:00

A 55M long recording is now available.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📚 Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html 2024-08-06T10:26:02+00:00

The concept of a genomics “Beacon” refers to facilitating connection between genomic data suppliers, developers, and researchers interested in acquiring genetic variation data. The Beacon system was intended to be simple: an API that allows users to query genomic data collections for the presence of specified genetic variations and receive a simple “Yes” or “No” response. The term “Beacon” was chosen to represent the goal of illuminating the hitherto opaque world of genetic data sharing through widespread engagement. The Beacon Project, which became one of the initial Global Alliance for Genomics and Health (GA4GH) Driver Projects, was warmly welcomed by both members of the GA4GH developer community and genomic resource providers Rambla et al. 2022.

Beacon v2 is a data query protocol and API that allows the researcher to seek information about specific genomic variants of biomedical research and clinical applications from the data providers (Beacon provider) without

This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.

Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ 🎥 Recording of M. tuberculosis Variant Analysis https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/recordings/#tutorial-recording-11-june-2024 2024-06-11T00:00:00+00:00

A 1H17M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ 🛠️ pox-virus-tiled-amplicon-ref-masking https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.html 2023-05-15T10:22:16+00:00

From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.

Viktoria Isabel Schwarz Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📚 Pox virus genome analysis from tiled-amplicon sequencing data https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html 2023-05-15T10:22:16+00:00

Pox viruses (Poxviridae) are a large family of viruses, and members of it have various vertebrate and arthropod species as their natural hosts. The most widely known species in the family are the now extinct variola virus from the genus orthopoxvirus as the cause of smallpox, and vaccinia virus, a related, likely horsepox virus, which served as the source for the smallpox vaccine that allowed eradication of that disease.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Tomas Klingström https://training.galaxyproject.org/training-material/hall-of-fame/TKlingstrom/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ 🎥 Recording of Trio Analysis using Synthetic Datasets from RD-Connect GPAP https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/recordings/#tutorial-recording-12-may-2023 2023-05-12T00:00:00+00:00

A 40M long recording is now available.

Jasper Ouwerkerk https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/ 🎥 Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/recordings/#tutorial-recording-10-may-2023 2023-05-10T00:00:00+00:00

A 55M long recording is now available.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📚 Avian influenza viral strain analysis from gene segment sequencing data https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html 2022-11-21T16:45:21+00:00

Of the four species of influenza viruses (Influenza A-D), Influenza A is the most virulent in human hosts and subtypes of it have been responsible for all historic flu pandemics.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ 🛠️ Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.html 2022-10-05T09:28:06+00:00

This workflow is created as part of a tutorial listed on GTN. The workflow shows the steps in human copy number variance detection using the Contrl_FREEC tool.

Human Copy Number Variations (hCNVs) are the result of structural genomic rearrangements that result in the duplication or deletion of DNA segments. These changes contribute significantly to human genetic variability, diseases, and somatic genome variations in cancer and other diseases Nam et al. 2015. hCNVs can be routinely investigated by genomic hybridisation and sequencing technologies

Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ David Salgado https://training.galaxyproject.org/training-material/hall-of-fame/d-salgado/ Krzysztof Poterlowicz https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ Simon Gladman https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 🛠️ Trio Analysis Tutorial https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.html 2022-05-19T12:25:33+00:00

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Jasper Ouwerkerk 📚 Trio Analysis using Synthetic Datasets from RD-Connect GPAP https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/tutorial.html 2022-05-19T12:25:33+00:00

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns. Some examples of these patterns are autosomal recessive, autosomal dominant, and de-novo variants, which are represented in the figure below. To elaborate, the most left tree shows an autosomal dominant inhertitance pattern where the offspring inherits a faulty copy of the gene from one of the parents. The center subfigure represents an autosomal recessive disease, here the offspring inherited a faulty copy of the same gene from both parents. In the right subfigure a de-novo mutation is shown, which is caused by a mutation during the offspring’s lifetime.

Jasper Ouwerkerk https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Jasper Ouwerkerk https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ ❓ TB Variant Report crashes (with an error about KeyError: 'protein') https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/faqs/key-error.html 2022-03-17T11:01:17+00:00

This is a bug present in TB Variant Report (aka tbvcfreport) version 0.1.8 and earlier. In this case it is triggered by the presence of variants in Rv3798. You only see this bug, however, if you forget to run tb_variant_filter (TB Variant Filter). Rv3798 is a suspected transposase and any variants in this gene region would be filtered out by tb_variant_filter, so if you see this crash, make sure you have run the filter step before the TB Variant Report step.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ ❓ Do I have to run the tools in the order of the tutorial? https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/faqs/tool_order.html 2022-03-02T15:46:20+00:00

The tools are presented in the order that a typical analysis would use. If you want to run some tools in parallel (to save time) you can do so. This workflow illustrates the analysis done in the tutorial and shows that there are multiple “paths” leading to outputs that have some steps that could be run at the same time: MultiQC, Kraken2, JBrowse and TB Variant Report.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ ❓ My snippy is running for a very long time. Is this normal? https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/faqs/runtime.html 2022-03-02T15:46:20+00:00

As this tutorial uses real world data some of the tools can run for quite a while. During a course we can expected longer run times as the Galaxy servers are heavily used. Typically expected runtimes are approximately:

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ 🎥 Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/recordings/#tutorial-recording-9-august-2021 2021-08-09T00:00:00+00:00

A 1H30M long recording is now available.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📚 Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html 2021-06-30T06:20:05+00:00

Sequence-based monitoring of global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for surveilling the emergence and spread of new viral variants, and for understanding the evolutionary dynamics of the virus.

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Jasper Ouwerkerk https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Beatriz Serrano-Solano https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/ 📰 New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org/training-material/news/2021/06/30/tutorial-sars-cov-2-variant-discovery.html 2021-06-30T00:00:00+00:00

Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 🛠️ vcf2lineage https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.html 2021-06-08T08:34:12+00:00

workflow-automation

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📚 Automating Galaxy workflows using the command line https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html 2021-06-08T08:34:12+00:00

Galaxy is well-known as a web-based data analysis platform which provides a graphical interface for executing common bioinformatics tools in a reproducible manner. However, Galaxy is not just a user-friendly interface for executing one tool at a time. It provides two very useful features which allow scaling data analyses up to a high-throughput level: dataset collections and workflows.

Simon Bray https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Martin Čech https://training.galaxyproject.org/training-material/hall-of-fame/martenson/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Armin Dadras https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ 🎥 Recording of Automating Galaxy workflows using the command line https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 30M long recording is now available.

Simon Bray https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/ 🎥 Recording of From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 15M long recording is now available.

Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ 🎥 Recording of M. tuberculosis Variant Analysis https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00

A 40M long recording is now available.

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ 🛠️ Identification of somatic and germline variants from tumor and normal sample pairs tutorial https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.html 2020-10-10T20:50:51+00:00

Identification of somatic and germline variants from tumor and normal sample pairs tutorial

🛠️ TB Variant Analysis v1.0 https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.html 2020-07-25T20:58:54+00:00

Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ 📚 M. tuberculosis Variant Analysis https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html 2020-07-25T20:58:54+00:00

Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease. The publication of the genome of M. tuberculosis H37Rv in 1998 gave researchers a powerful new tool for understanding this pathogen. This genome has been revised since then, with the latest version being available

Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ Simon Gladman https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ Thoba Lose https://training.galaxyproject.org/training-material/hall-of-fame/thobalose/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Linelle Abueg https://training.galaxyproject.org/training-material/hall-of-fame/abueg/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Mélanie Petera https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/ 🛠️ Simple COVID-19 - PE Variation https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.html 2020-06-24T15:38:29+00:00

Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured

📚 From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html 2020-06-24T15:38:29+00:00

The aim of this tutorial is twofold:

Marius van den Beek https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/ Dave Clements https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/ Daniel Blankenberg https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Mélanie Petera https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ 🛠️ Calling variants in non-diploid systems https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/workflows/Calling_variants_in_non-diploid_systems.html 2020-03-15T19:26:44+00:00

Calling variants in non-diploid systems

Anton Nekrutenko Alex Ostrovsky 🛠️ Exome Seq Training Full W Cached Ref https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.html 2019-06-26T17:26:19+00:00

Exome sequencing data analysis for diagnosing a genetic disease

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 🛠️ Exome Seq Training Pre-Mapped W Cached Ref https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_from_premapped.html 2019-06-26T17:26:19+00:00

Exome sequencing data analysis for diagnosing a genetic disease; short version starting from pre-mapped reads

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ 📚 Identification of somatic and germline variants from tumor and normal sample pairs https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/tutorial.html 2019-03-13T10:31:31+00:00

When sequencing genomic material from a human tumor, the underlying clinical or

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Simon Gladman https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ 🛠️ diploid https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/workflows/diploid.html 2019-01-03T07:57:50+00:00

Calling variants in diploid systems

Anton Nekrutenko Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ 🛠️ Du Novo GTN Tutorial - Variant Calling https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.html 2018-08-17T11:18:16+00:00

Run this on the trimmed consensus reads (DCS or SSCS) from Du Novo.

🛠️ Du Novo GTN Tutorial - Make Consensus Sequences https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/dunovo.html 2018-08-17T11:18:16+00:00

Run this on raw duplex sequencing reads to produce duplex consensus sequences.

🛠️ Microbial Variant Calling https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.html 2018-04-06T19:46:09+00:00

Microbial Variant Calling

🛠️ Mapping And Molecular Identification Of Phenotype Causing Mutations https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.html 2018-03-16T10:56:52+00:00

Reproduce the tutorial analysis at https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html

📚 Mapping and molecular identification of phenotype-causing mutations https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html 2018-03-07T15:58:55+00:00

In order to map and identify phenotype-causing mutations efficiently from a

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ 📚 Microbial Variant Calling https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html 2018-02-26T16:12:34+00:00

Variant calling is the process of identifying differences between two genome samples. Usually differences are limited to single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). Larger structural variation such as inversions, duplications and large deletions are not typically covered by “variant calling”.

Anna Syme https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/ Simon Gladman https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ Torsten Seemann https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/ Jennifer Hillman-Jackson https://training.galaxyproject.org/training-material/hall-of-fame/jennaj/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Simon Gladman https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ Peter van Heusden https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ 📚 Calling very rare variants https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/tutorial.html 2017-02-22T11:51:41+00:00

This page explains how to perform discovery of low frequency variants from duplex sequencing data. As an example we use the ABL1 dataset published by Schmitt and colleagues (SRA accession SRR1799908).

Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ Nick Stoler https://training.galaxyproject.org/training-material/hall-of-fame/NickSto/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Mateo Boudet https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/ Alexandre Cormier https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ 📚 Calling variants in diploid systems https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/tutorial.html 2017-02-20T22:21:58+00:00

Today we hear a lot about personalized medicine. Yet the personalization is defined by the genetic make up of the individual. In this tutorial we will discuss how this information can be uncovered from the genomic sequencing data.

Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ 📚 Calling variants in non-diploid systems https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html 2017-02-16T16:45:19+00:00

The majority of life on Earth is non-diploid and represented by prokaryotes, viruses, and their derivatives, such as our own mitochondria or plant’s chloroplasts. In non-diploid systems, allele frequencies can range anywhere between 0 and 100% and there could be multiple (not just two) alleles per locus. The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ Alex Ostrovsky https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Alex Ostrovsky https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/ Mélanie Petera https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/ Nate Coraor https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Vijay https://training.galaxyproject.org/training-material/hall-of-fame/nvk747/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ 🖼️ Introduction to Variant analysis https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/introduction/slides.html 2016-08-19T14:05:48+00:00

What is Exome sequencing?

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Ekaterina Polkh https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ 📚 Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html 2016-08-19T14:05:48+00:00

Exome sequencing is a method that enables the selective sequencing of the

Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Torsten Houwaart https://training.galaxyproject.org/training-material/hall-of-fame/torhou/ Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Ekaterina Polkh https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/ Martin Čech https://training.galaxyproject.org/training-material/hall-of-fame/martenson/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Armin Dadras https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/