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/. An index of the microbial ENA/SRA (Dec 2016) can be queried at http://www.bigsi.io.
You can read more in the publication.
See: https://bigsi.readme.io/docs for install instructions.
Quickstart available at https://bigsi.readme.io/docs/your-first-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.