gaybro8777 / bigsi

BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data

BItsliced Genomic Signature Index [BIGSI]

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.

Install

See: https://bigsi.readme.io/docs for install instructions.

Quickstart

Quickstart available at https://bigsi.readme.io/docs/your-first-bigsi

Citation

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.