Variant Analysis — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoBérénice Batut avatar Bérénice BatutAnton Nekrutenko avatar Anton Nekrutenkoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBjörn Grüning avatar Björn Grüning

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members Done ✅ (4 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Done ✅ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (3 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Pending ❌ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.

Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Variant analysis ❌ ❌ ❌ ✅ ❌
Calling variants in diploid systems ❌ ❌ ❌ ✅ ❌
Calling variants in non-diploid systems ❌ ❌ ❌ ✅ ❌
Calling very rare variants ❌ ❌ ❌ ✅ ❌
Microbial Variant Calling ❌ ❌ ❌ ✅ ❌
Mapping and molecular identification of phenotype-causing mutations ❌ ❌ ❌ ✅ ❌
Avian influenza viral strain analysis from gene segment sequencing data ❌ ❌ ❌ ✅ ❌
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis ✅ ❌ ❌ ✅ ❌
M. tuberculosis Variant Analysis ❌ ❌ ❌ ✅ ❌
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data ✅ ✅ ❌ ✅ ❌
Pox virus genome analysis from tiled-amplicon sequencing data ✅ ✅ ❌ ✅ ❌
Exome sequencing data analysis for diagnosing a genetic disease ❌ ❌ ❌ ✅ ❌
Identification of somatic and germline variants from tumor and normal sample pairs ❌ ❌ ❌ ✅ ❌
Somatic Variant Discovery from WES Data Using Control-FREEC ❌ ❌ ❌ ✅ ❌
Trio Analysis using Synthetic Datasets from RD-Connect GPAP ❌ ❌ ❌ ✅ ❌
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 ❌ ✅ ❌ ✅ ❌

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Calling variants in diploid systems Diploid Dec 21, 2024 3 ❌ ❌ ❌
Calling variants in non-diploid systems Calling variants in non-diploid systems Dec 21, 2024 2 ✅ ❌ ❌
Calling very rare variants Du Novo GTN Tutorial - Make Consensus Sequences Dec 21, 2024 3 ❌ ❌ ❌
Calling very rare variants Du Novo GTN Tutorial - Variant Calling Dec 21, 2024 3 ❌ ❌ ❌
Microbial Variant Calling Microbial Variant Calling Dec 21, 2024 4 ✅ ❌ ❌
Mapping and molecular identification of phenotype-causing mutations Mapping And Molecular Identification Of Phenotype Causing Mutations Dec 21, 2024 3 ❌ ❌ ❌
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Simple COVID-19 - PE Variation Dec 21, 2024 1 ❌ ❌ ❌
M. tuberculosis Variant Analysis TB Variant Analysis v1.0 Dec 21, 2024 7 ✅ ✅ ❌
Pox virus genome analysis from tiled-amplicon sequencing data pox-virus-tiled-amplicon-ref-masking Dec 21, 2024 2 ✅ ❌ ❌
Exome sequencing data analysis for diagnosing a genetic disease Exome Seq Training Pre-Mapped W Cached Ref Dec 21, 2024 5 ✅ ❌ ❌
Exome sequencing data analysis for diagnosing a genetic disease Exome Seq Training Full W Cached Ref Dec 21, 2024 5 ✅ ❌ ❌
Identification of somatic and germline variants from tumor and normal sample pairs Identification of somatic and germline variants from tumor and normal sample pairs tutorial Dec 21, 2024 1 ✅ ❌ ❌
Somatic Variant Discovery from WES Data Using Control-FREEC Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC Dec 21, 2024 1 ✅ ❌ ❌
Trio Analysis using Synthetic Datasets from RD-Connect GPAP Trio Analysis Tutorial Dec 21, 2024 5 ✅ ❌ ❌

Your topic's Workflow Testing Results

Coming Soon™

Learning Pathways using materials from this Topic

Statistics for your Learning Pathways
Stats powered by Plausible Analytics

Events using materials from this Topic

TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

Statistics For Your Materials

Stats powered by Plausible Analytics