alexpreynolds / kmer-counter-sparse

Count canonical kmers with Google sparse_hash_map

kmer-counter-sparse

The kfs program reads in multiline FASTA records, counts canonical kmers using Google's sparse_hash_map hash table, and measures time taken to read in and process records.

Usage

To install sparse_hash_map libraries on OS X, use Homebrew: brew install google-sparsehash.

Compilation

$ make kfs

Performance

Specify variables K (integer) and FASTA (path to FASTA sequences).

$ /usr/bin/time -l ./kfs -k ${K} -i ${FASTA}
...