GalaxyProject MPXV analysis effort

Overview

Workflows

Here is the info to get you started quickly:

  • We have three workflows for analysis of Illumina data (Oxford nanopore workflows can also be added. Request here).
  • Workflows can be used to analyze any number of samples.
  • Workflows can be used via graphical user interface right now on any of our public instances in EU (https://usegalaxy.eu), US (https://usegalaxy.org), or Australia (https://usegalaxy.org.au).
  • We provide powerful computational infrastructure for data analysis supported by national supercomputing resources in the US, EU, and Australia.

Workflows for discovery of sequence variants

We developed two workflows for the analysis of Monkeypox Virus (MPXV) sequencing data. The workflows are available from WorkflowHub.

Link Workflow Inputs Outputs Aligner Caller
WorkflowHub Illumina metatranscriptomic PE:
Variant analysis from metatranscriptomic data.
ILL-PE		 1. Paired reads [fastqsanger]
2. MPXV reference [genbank]		 Variants [vcf] BWA MEM lofreq
WorkflowHub Report generation:
Generation of final variant analysis reports/plots.
REPORTING		 Variants [vcf] Reports [tsv] - -
WorkflowHub Consensus building:
Generation of consensus sequences from VCF datasets.
CONSENSUS		 Variants [vcf] Consensus [multi fasta] - -

vcf = variant call format, tsv = TAB-separated values, fastqsanger = fastq format with Sanger encoding of base quality values.

Workflows are designed to be used one after another:

  1. Run the ILL-PE workflow to generate lists of variants.
  2. Run the REPORTING workflow on variants generated above to produce variant tables.
  3. Run the REPORTING workflow on variants generated above (#1) to produce consensus sequences.

WorkflowHub offers a convenient Run on usegalaxy.eu option from the workflow pages. Users of other Galaxy servers can go to Workflow -> Import on their server and paste the following links as an Archived Workflow URL: