ska - 1.0+dfsg-2 main

SKA (Split Kmer Analysis) is a toolkit for prokaryotic (and any other
small, haploid) DNA sequence analysis using split kmers. A split kmer is
a pair of kmers in a DNA sequence that are separated by a single base.
Split kmers allow rapid comparison and alignment of small genomes, and
is particulalry suited for surveillance or outbreak investigation. SKA
can produce split kmer files from fasta format assemblies or directly
from fastq format read sequences, cluster them, align them with or
without a reference sequence and provide various comparison and summary
statistics. Currently all testing has been carried out on high-quality
Illumina read data, so results for other platforms may vary.