BIGSI (described below) is now superceded by COBS https://github.com/iqbal-lab-org/cobs
BIGSI can search a collection of raw (fastq/bam), contigs or assembly for genes, variant alleles and arbitrary sequence. It can scale to millions of bacterial genomes requiring ~3MB of disk per sample while maintaining millisecond kmer queries in the collection.
Documentation can be found at https://bigsi.readme.io/.
You can read more in the publication.
See: https://github.com/iqbal-lab-org/BIGSI/wiki/Installation for install instructions.
Quickstart available at https://github.com/iqbal-lab-org/BIGSI/wiki/Constructing-a-BIGSI
Please cite
Ultra-fast search of all deposited bacterial and viral genomic data
Phelim Bradley, Henk den Bakker, Eduardo Rocha, Gil McVean, Zamin Iqbal
Nature Biotechnology; doi: http://dx.doi.org/10.1038/s41587-018-0010-1
if you use BIGSI in your work.