Task: mapreads

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martinghunt edited this page Aug 12, 2015 · 1 revision

Task: mapreads

This task uses BWA MEM to map reads to contigs, making a sorted by coordinate and indexed BAM file.

Usage and options

The general usage is

circlator mapreads [options] <reference.fasta> <reads.fasta/q> <out.bam>

The reads can be in any format that BWA MEM accepts (eg FASTA, FASTQ and optionally gzipped).

There are the following options:

--bwa_opts: options to pass to BWA mem, in quotes. Default: "-x pacbio".
--threads: the number of threads to use with BWA and samtools. Default: 1.
--verbose: output progress messages. Default is to be silent.

Output files

The output is a sorted by coordinate and indexed BAM file out.bam, and its index file out.bam.bai.