remove host

virpipe remove-host --image IMAGE --prefix PREFIX \
                           [--outdir OUTDIR] [--resume] \
                           --platform [{illumina,nanopore}] \
                           --fastq FASTQ [--fastq2 FASTQ2] \
                           --host-genome [HOST_GENOME]

The task remove-host is for getting rid of host-derived reads from the input. Input reads are mapped to the host genome, and not mapped reads are extracted as output in .fastq format.

Used tools

Minimap2, bedtools, samtools

Options

• --host-genome: (File) Host genome sequence in FASTA format.