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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>



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