Pipeline output

:package: full output (v.0.3.2) an archive of the output produced by the pipeline is available

:mag: a browsable output (v.0.1.0) is available for a preview, although for space reasons not all attachments are available.

Description

The pipeline will produce a directory with the following subdirectories:

  • fastp_qc (with the QC metrics)
  • assembly (with the contigs produced by Megahit)
  • mining (with the output of phigaro, vibrant, virfinder, virsorter)
  • prodigal (with the gene prediction)
  • cd-hit (with the dereplicated vOTUs)
  • taxonomy (with the output of Kraken2 and Krona)
  • report (with the interactive HTML report)

The report not only summarises graphically the output of the pipeline, but also contains hyperlinks to relevant files:

  • The count table
  • The taxonomy table
  • PhyloSeq object
  • PhyloSeq object, with normalized counts (css)
  • The multifasta set of viral OTUs
  • The multifasta set of proteins predicted in the viral OTUs
  • The annotation (GFF) of the viral OTUs