SYNOPSIS

mapMers-depth {-count|-depth|-stats} -mers MERYL -m MERSIZE -seq IN.FASTA

OPTIONS

Modes of operation

For sequence ordinal 's' and position in that sequence 'p':

-count

reports the count (c) of the single kmer that starts at position (p).

Format: 's p c'

-depth

reports the number (n) of kmers that span position (p).

Format: 's p n'

-stats

reports the minimum (m), maximum (M), and average (a) count of all mers that span position (p). also reports total count (t) and number of kmers (n)

Format: 's p m M a t n'

General

-m MERSIZE

-mers MERYL

meryl(1) database

-seq IN.FASTA

fasta input sequence