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 logoAnika Erxleben avatar Anika Erxlebenorcid logoPolina Polunina avatar Polina Poluninaorcid logoTomas Klingström avatar Tomas Klingströmorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoJörg Wennmann avatar Jörg WennmannMélanie Pétéra avatar Mélanie Pétéraorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton NekrutenkoVerena Moosmann avatar Verena Moosmannorcid logoLinelle Abueg avatar Linelle AbuegJasper Ouwerkerk avatar Jasper OuwerkerkTorsten Houwaart avatar Torsten Houwaartorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoNick Stoler avatar Nick Stolerorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoArmin Dadras avatar Armin Dadrasorcid logoSaim Momin avatar Saim MominAlan Rubin avatar Alan RubinNick Moore avatar Nick MooreNiall Beard avatar Niall Beardorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoTeresa Müller avatar Teresa MüllerGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoNiklas Mayle avatar Niklas Mayleorcid logoAnna Syme avatar Anna Symeorcid logoHelena Rasche avatar Helena RascheEkaterina Polkh avatar Ekaterina Polkhorcid logoMartin Čech avatar Martin Čechorcid logoBérénice Batut avatar Bérénice Batutorcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBjörn Grüning avatar Björn Grüningorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoMarius van den Beek avatar Marius van den Beekorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMaria Doyle avatar Maria Doyleorcid logoNicola Soranzo avatar Nicola SoranzoThoba Lose avatar Thoba LoseDavid Salgado avatar David Salgadoorcid logoDave Clements avatar Dave ClementsTorsten Seemann avatar Torsten SeemannSimon Bray avatar Simon Bray

Funding

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

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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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ELIXIR Europe
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Melbourne Bioinformatics
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UFR
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The University of Melbourne
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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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de.NBI
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Australian BioCommons
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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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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