SARS-CoV-2 processing requests

Request execution of Galaxy SARS-CoV-2 variation analysis workflows on input data you provide.

Prerequisites

This automation system is set up to work with ARTIC-amplified paired-end Illumina sequence data, the most common type of SARS-CoV-2 sequencing data today.

Usage

• Fork the repo and create a new file in the file_requests/ directory.
  • The file should contain a header line, followed by a list of web links to the files you want to analyze. See the example file provided.
  • Links need to be formatted as follows: <base_url>/<sample ID>_[12].<file_extension> (1 representing the forward strand and 2 the reverse strand of paired-end data). If your data is not accessible in this way, or unpublished, it's not a problem - just create an issue and describe what you need.
• Create a PR with your changes. We will review and merge it as soon as possible.

Analysis of your data

• After merging, the data will be uploaded to Galaxy Europe and processed by our collection of SARS-CoV-2 genomic sequence analysis workflows, which will produce highly-sensitive per-sample variant calls, per-batch variant reports and reliable consensus sequences for all your samples.

• Depending on the amount of other jobs running on our server and on the size of your data batch, processing may take between a few hours and a day.

• Once ready, the complete analysis will become available as a set of published histories on the server.

  💡 Hint: Your histories will carry the filename from your pull request in their name.

• Key result files - BAM, VCF and consensus sequence FASTA files for each sample in your batch - will also be pushed automatically to a publicly readable FTP server hosted by BSC.

• After a few days your results will also be included in the viral Beacon project dashboard.

Links

• Documentation for the project
• Scripts for our analysis bot
• planemo and bioblend tools powering the automation of the analyses.

The analyses will be performed using the Galaxy platform and open source tools from BioConda and BioContainers. The workflows will run on the de.NBI-cloud and form part of the Galaxy COVID-19 efforts with partners around the world. For more information please visit https://github.com/galaxyproject/SARS-CoV-2.