galaxyproject / galaxyproject/training-material

Needed: SARS-CoV-2 amplicon variant analysis tutorial needed

Open
#2,546 1 comment 3 reactions 0 assignees View on GitHub
new tutorial tutorial request
Dominant language
HTML
Stars
367
Forks
1.1k
Avg merge
16h 27m
Merged PRs (30d)
49

Description

The existing [SARS-CoV-2 variant analysis] tutorial is focused on the analysis of metagenomic sequencing data. The majority of data being produced, however, uses the ARTIC amplicon protocol (for Illumina and Nanopore). The [RECoVERY](https://www.biorxiv.org/content/10.1101/2021.01.16.425365v2.full), [SANBI](https://galaxy.sanbi.ac.za/workflows/list_published?__identifer=ffcdtn4xsl) and the [Galaxy COVID-19 project](https://covid19.galaxyproject.org/artic/#analyzing-artic-data-with-galaxy) have produced workflows for SARS-CoV-2 amplicon analysis.

A new tutorial is needed walking through at least one of these workflows. It can also mention the use of Nextclade and Pangolin.

I (@pvanheus) propose to develop such a tutorial and refine it during the ASBCB Omics Codeathon: https://datascience.nih.gov/news/participant-applications-asbcb-omics-codeathon in June.

To fill out that form, enter your details, mention the Galaxy SARS-CoV-2 Amplicon tutorial and then select:
1. Would you like to pitch a project idea for the codeathon: *No*
2. Would you be interested in being a team lead for a project *No*
3. Here are some approximate project titles, please pick the top three you are interested in working on *New projects as they arise*

(this last one because our project is not on the official list (yet))

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.