Documentation

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.


bloombuild

Usage

buildbloom k fp ref

Arguments

k

The size of K-mers (words) to insert into the Bloom filter. We recommend 21.

fp

Accepted false positive probability in the Bloom filter. We have used 0.0005

ref

A file with filenames for reference genomes to be stored in the Bloom filter.

outfile

A filename for the newly created Bloom filter.


facs

Usage

facs k filterlist queries

Arguments

k

Same k as was used in the filters you load. All loaded filters need to have the same k.

filterlist

File with a list of filters to load, one file per line.

queries

Fasta file with reads to be classified.

outprefix

The three output files will be named using this filename prefix.