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 If your data is not accessible in this way, or unpublished, it's not a problem - just create an issue and describe what you need.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.

GitHub

https://github.com/usegalaxy-eu/sars-cov-2-processing-requests