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@hoelzer hoelzer released this 05 Jun 11:16
· 237 commits to master since this release
v0.1
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Learn about vigilant mode.

This is a first release candidate of the EBI metagenomics virus detection and classification pipeline.

The pipeline is implemented in Nextflow and CWL based on the same core Python and Shell scripts and Docker containers.

The pipeline features

  • length filtering of the input assembly
  • detection of potential viral sequences with VirSorter, VirFinder, and PPR-Meta
  • classification of potential viruses into high and low confidence sets as well as prophages
  • ORF prediction
  • protein detection w/ hmmscan using a customized database of virus-specific profile HMMs (so-called ViPhOGs)
  • filtering of the hits and taxonomic assignment based on a voting system
  • visualization of the results with Krona, Sankey (currently only in the Nextflow pipeline), and ChromoMap (Nextflow)
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