2 hours ago by
United States
From BBMap suite.
$ kmercountexact.sh
Written by Brian Bushnell
Last modified November 29, 2018
Description: Counts the number of unique kmers in a file.
Generates a kmer frequency histogram and genome size estimate (in peaks output),
and prints a file containing all kmers and their counts.
Supports K=1 to infinity, though not all values are allowed.
SEE ALSO: bbnorm.sh/khist.sh loglog.sh, and kmercountmulti.sh.
Usage: kmercountexact.sh in=<file> khist=<file> peaks=<file>
Input may be fasta or fastq, compressed or uncompressed.
Output may be stdout or a file. out, khist, and peaks are optional.
or
$ kmercountmulti.sh
Written by Brian Bushnell
Last modified December 30, 2016
Description: Estimates cardinality of unique kmers in sequence data.
Processes multiple kmer lengths simultaneously to produce a histogram.
Usage: kmercountmulti.sh in=<file> sweep=<20,100,8> out=<histogram output>
