map

virpipe map --image IMAGE --prefix PREFIX [--outdir OUTDIR] \
                   [--resume] --platform [{illumina,nanopore}] \
                   --fastq FASTQ [--fastq2 FASTQ2] \
                   [--ref [REF ...]] [--dir-ref [DIR_REF]] \
                   [--min-avg-cov 1.0]

The task map is for mapping input reads onto given reference sequence(s). Reference(s) can be given as fasta files or a directory containing fasta files. Output files include the summary of mapping statistics for each reference generated by Bamcov({prefix}.map.txt) and mapping reports for each reference generated by Qualimap in pdf format.

Used tools

Minimap2, Bamcov, Qulimap

Options

• --ref: (File) Reference sequence(s) in FASTA format. Multiple files can be given by delimiting them with a blank. For example, --ref virus1.fasta virus2.fasta
• --dir-ref: (Directory) Reference sequence(s) given as a directory. All .fasta and .fa files under this directory will be given as references.
• --min-avg-cov: (Float, default 1.0) VirPipe filters mapping summary for each reference with the value in 'AVG_COV'(average coverage) column. The value for this option is used as a threshold. 'AVG_COV' is calculated by dividing the sum of the number of bases of all mapped reads by the length of reference sequence.