p3-genome-kmer-hits

Count KMER Hits in Genomes

p3-genome-kmer-hits.pl [options] kmerDB

This script takes as input a list of genome IDs and outputs a table of the number of kmer hits by group in each genome. The output file will be tab-delimited, with the genomeID, the sequence ID, the group ID, the group name, and the kmer hit count.

Parameters

The positional parameter is the file name of the kmer database. This is a json-format KmerDb object.

The standard input can be overridden using the options in Input Options.

Additional command-line options are those given in Column Options (to choose the genome ID column) plus the following options.

• prot

If specified, the kmers are assumed to be protein kmers.

• pegs

If specified, the kmer hits will be counted against the genome’s proteins, not the genome itself. This implies --prot.

• verbose

If specified, progress messages will be written to STDERR.