variant-analysis

Tutorials covering variant-analysis

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Using Galaxy and Managing your Data

Lesson Slides Hands-on Recordings Input dataset Workflows
Automating Galaxy workflows using the command line
workflows variant-analysis covid19

Variant Analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Variant analysis
Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)
Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
Avian influenza viral strain analysis from gene segment sequencing data
virology one-health
Calculating CHEK2 variant effect scores from MAVE data with CountESS
MAVE DMS variant effect functional genomics clinical genomics
Calling variants in diploid systems
Calling variants in non-diploid systems
prokaryote microgalaxy
Calling very rare variants
Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
Exome sequencing data analysis for diagnosing a genetic disease
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
covid19 virology one-health
Identification of somatic and germline variants from tumor and normal sample pairs
M. tuberculosis Variant Analysis
prokaryote one-health microgalaxy tuberculosis
Mapping and molecular identification of phenotype-causing mutations
Microbial Variant Calling
prokaryote microgalaxy gmod jbrowse1
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
covid19 virology one-health
Pangenome variant calling with DeepVariant
pangenome
Pox virus genome analysis from tiled-amplicon sequencing data
virology one-health
Somatic Variant Discovery from WES Data Using Control-FREEC
Trio Analysis using Synthetic Datasets from RD-Connect GPAP
cyoa

Contributors

This material was contributed to by:

orcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBjörn Grüning avatar Björn Grüningorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoPolina Polunina avatar Polina Poluninaorcid logoMarius van den Beek avatar Marius van den Beekorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoHelena Rasche avatar Helena RascheSimon Bray avatar Simon Brayorcid logoSaim Momin avatar Saim MominTorsten Houwaart avatar Torsten Houwaartorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoEkaterina Polkh avatar Ekaterina Polkhorcid logoBérénice Batut avatar Bérénice Batutorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoMaria Doyle avatar Maria DoyleGildas Le Corguillé avatar Gildas Le Corguilléorcid logoDave Clements avatar Dave Clementsorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoAnna Syme avatar Anna SymeAlan Rubin avatar Alan RubinTorsten Seemann avatar Torsten Seemannorcid logoSaskia Hiltemann avatar Saskia HiltemannDavid Salgado avatar David SalgadoNiall Beard avatar Niall Beardorcid logoNiklas Mayle avatar Niklas Mayleorcid logoSimon Gladman avatar Simon Gladmanorcid logoNicola Soranzo avatar Nicola SoranzoNick Moore avatar Nick MooreThoba Lose avatar Thoba LoseJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoPeter van Heusden avatar Peter van HeusdenMélanie Pétéra avatar Mélanie Pétéraorcid logoTomas Klingström avatar Tomas Klingströmorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoTeresa Müller avatar Teresa Müllerorcid logoLinelle Abueg avatar Linelle Abuegorcid logoKatarzyna Kamieniecka avatar Katarzyna KamienieckaVerena Moosmann avatar Verena Moosmannorcid logoMartin Čech avatar Martin ČechNick Stoler avatar Nick Stolerorcid logoArmin Dadras avatar Armin DadrasAnton Nekrutenko avatar Anton Nekrutenkoorcid logoJörg Wennmann avatar Jörg Wennmannorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

These individuals or organisations provided funding support for the development of this resource

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Melbourne Bioinformatics
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BeYond-COVID
BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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DEFEND
DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe. This work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 773701.
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ELIXIR-CONVERGE
ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement № 871075
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Australian BioCommons
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de.NBI
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The University of Melbourne
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ELIXIR Europe
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UFR