ska alleles - simonrharris/SKA GitHub Wiki
The alleles subcommand creates split kmer files from multifasta files (i.e. fasta files containing one or more sequences).
While ska fasta creates a split kmer file containing a single sample with all split kmers from all fasta files provided to it, ska alleles creates a file with one sample per sequence in the fasta file(s).
ska fasta [options] <fasta files>
Options:
-h Print this help.
-f <file> File of split kmer file names. These will be added to or
used as an alternative input to the list provided on the
command line.
-k <int> Split Kmer size. The kmer used for searches will be twice
this length, with the variable base in the middle. e.g. a
kmer of 15 will search for 31 base matches with the middle
base being allowed to vary. Must be divisible by 3.
[Default = 15]