preprocess

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

The task preprocess is for filtering input reads depending on their quality or read length and trimming adapter sequences.

Used tools

• Nanopore: Nanofilt
• Illumina: PrinSeq, Trimmomatic

Options

• --nanopore-min-read-quality: (Int, default 8) Threshold for read quality filtering for nanopore reads.
• --nanopore-min-read-length: (Int, default 200) Threshold for read length filtering for nanopore reads.
• --illumina-min-read-quality: (Int, default 8) Threshold for read quality filtering for illumina reads.