qc

virpipe qc --image IMAGE --prefix PREFIX [--outdir OUTDIR] \
                  [--resume] --platform [{illumina,nanopore}] \
                  --fastq FASTQ [--fastq2 FASTQ2] \
                  [--nanopore-min-read-quality 8] \
                  [--nanopore-min-read-length 200]

The task qc is for producing a quality control report for input reads.

Used tools

• Nanopore: NanoPlot
• Illumina: FastQC, MultiQC

Options

• --nanopore-min-read-quality: (Int, default 8) For nanopore reads, QC statistics are calculated only with the reads with the quality score over this value.
• --nanopore-min-read-length: (Int, default 200) For nanopore reads, QC statistics are calculated only with the reads with the read length over this value.