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
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
Pox virus genome analysis from tiled-amplicon sequencing data
virology one-health
Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)
Somatic Variant Discovery from WES Data Using Control-FREEC
Trio Analysis using Synthetic Datasets from RD-Connect GPAP
cyoa
Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons

Contributors

This material was contributed to by:

Gildas Le Corguillé avatar Gildas Le CorguilléAlan Rubin avatar Alan RubinVerena Moosmann avatar Verena Moosmannorcid logoWolfgang Maier avatar Wolfgang MaierSimon Bray avatar Simon BrayMélanie Petera avatar Mélanie Peteraorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnna Syme avatar Anna Symeorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoArmin Dadras avatar Armin Dadrasorcid logoSimon Gladman avatar Simon Gladmanorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMartin Čech avatar Martin ČechNick Stoler avatar Nick Stolerorcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoLinelle Abueg avatar Linelle AbuegTorsten Houwaart avatar Torsten Houwaartorcid logoHelena Rasche avatar Helena RascheDavid Salgado avatar David Salgadoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauTorsten Seemann avatar Torsten Seemannorcid logoAlex Ostrovsky avatar Alex OstrovskyThoba Lose avatar Thoba LoseJasper Ouwerkerk avatar Jasper OuwerkerkMarius van den Beek avatar Marius van den Beekorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoJörg Wennmann avatar Jörg Wennmannorcid logoDave Clements avatar Dave Clementsorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoPolina Polunina avatar Polina Poluninaorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoDaniel Blankenberg avatar Daniel BlankenbergNick Moore avatar Nick MooreNiall Beard avatar Niall Beardorcid logoTeresa Müller avatar Teresa MüllerEkaterina Polkh avatar Ekaterina Polkhorcid logoBérénice Batut avatar Bérénice Batutorcid logoTomas Klingström avatar Tomas KlingströmAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria Doyleorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoBjörn Grüning avatar Björn Grüningorcid logoTristan Reynolds avatar Tristan Reynolds

Funding

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

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