ska fasta - simonrharris/SKA GitHub Wiki
The fasta subcommand creates a split kmer file from one or more fasta files.
The command creates a split kmer file containing a single sample with all split kmers from all fasta files provided to it. To create separate split kmer files for each sequence in a fasta file, use ska alleles instead.
The -c flag informs SKA that all contigs in the input file are circular, which will result in kmers that span the two ends of the sequence.
ska fasta [options] <fasta files>
Options:
ska fasta [options] <fasta files>
Options:
-c Treat all contigs as circular.
-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]
-o <file> Output file prefix. [Default = fasta]