COVID-19 sequence analysis on Illumina Amplicon PE data

This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf, covid-19-signal and the Thiagen Titan workflow. These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK, CanCOGeN and some US state public health laboratories.

This workflow is also the subject of a Galaxy Training Network tutorial (currently a Work in Progress). It differs from this workflow in that it does not use lofreq and is aimed at rapid analysis of majority variants and lineage/clade assignment with pangolin and nextclade.

TODO:

1. Add support for QC using negative and positive controls
2. Integrate with phylogeny tools including IQTree and UShER (and possibly more).

Changelog

[0.3] 2022-11-22

• update all tools:
  • fastp from 0.20.1 to 0.23.2
  • bwa_mem from 0.7.17.1 to 0.7.17.2
  • samtools_stats from 2.0.2 to 2.0.4
  • samtools_view from 1.9 to 1.15.1
  • ivar_trim from 1.3.1 to 1.4.2
  • ivar_variants from 1.3.1 to 1.4.2
  • ivar_consensus from 1.3.1 to 1.4.2
  • multiqc from 1.9 to 1.11
  • pangolin from 3.1.14 to 4.3
  • nextclade from 1.4.1 to 2.7.0

[0.2.3] 2022-05-25

Changed

• Changed creator ORCID to absolute URI

[0.2.2] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

[0.2.1] 2021-11-04

Added

• Added .workflowhub.yml

[0.2] - 2021-10-13

Changed

• Upgrade pangolin to 3.1.14
  • this is a bugfix release that addresses problems with commas in sequence IDs
• Upgrade nextclade to 1.4.1
  • nextclade has a new way of dealing with the nextclade database, so it is now downloaded using nextclade itself
  • the latest release supports detecting and reporting frameshifts
  • version 1.4.1 fixes a problem with formatting columns that was present in previous versions
• A header line is now part of the tabular reports produced by both pangolin and nextclade
• The aligned primer-trimmed reads BAM and the multi-fasta combined consensus genomes datasets are no longer hidden as part of the workflow execution

[0.1] - 2021-06-20

• Initial version of SARS-CoV-2 Illumina Amplicon pipeline - iVar based for IWC

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
• toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
• toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4
• toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
• toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0
• __FLATTEN__
• toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.2+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
• toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0