FACS is a system of two utilitites: bloombuild for assembling filters from genome sequences and facs for applying a filter to a file of sequence reads.
buildbloom k fp ref
The size of K-mers (words) to insert into the Bloom filter. We recommend 21.
Accepted false positive probability in the Bloom filter. We have used 0.0005
A file with filenames for reference genomes to be stored in the Bloom filter.
A filename for the newly created Bloom filter.
facs k filterlist queries
Same k as was used in the filters you load. All loaded filters need to have the same k.
File with a list of filters to load, one file per line.
Fasta file with reads to be classified.
The three output files will be named using this filename prefix.