EnumerateNullomers

Extracts all nullomers, and enumerates all present kmers, of a specified kmer length from a fasta sample.

Required arguments:

Argument	Explanation
–genome_filepath	Path to the fasta file containing the genome being analyzed.*
–nullomer_output_filepath	Path to the output .txt file where the nullomers absent from the supplied genome will be written, with one nullomer written on each line.
–kmer_output_filepath	Path to the output .tsv file where the kmers, and their corresponding occurrence counts, from the supplied genome will be written.
–kmer_length	Length of kmers/nullomers to be enumerated.

Outputs:

• Text file containing a list of nullomers absent from the supplied genome file.

• Text file containing every kmer occuring at least once in the genome file supplied, accompanied by a count of how often each occur

Note

^* This file must be formatted such that the FASTA headers read “>chr1”, “>chr2”, “>chr3”, …