SYNOPSIS

reapr perfectmap <assembly.fa> <reads_1.fastq> <reads_2.fastq> <avginsertsize> <outprefix>

DESCRIPTION

Note: the reads can be gzipped. If the extension is '.gz', then they are assumed to be gzipped and dealt with accordingly (i.e. called something like <reads_1.fastq.gz> <reads_2.fastq.gz>).

Important

all reads must be the same length.