Skip to content
BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data
Branch: master
Clone or download
Latest commit 1920b06 Feb 7, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
.conda Add conda install yamls and bigsi param calc R script Dec 10, 2018
example-data Add read only option Jan 29, 2019
example-scripts Update example scripts Feb 2, 2019
.gitignore Test end to end bloom build lookup Nov 25, 2018
.travis.yml Update travis config Feb 2, 2019
Dockerfile Remove pyseqfile as requirement Dec 1, 2018
LICENSE Update Feb 7, 2019
VERSION cbg->bigsi Dec 11, 2017
docker_compose_test.yaml Skip rocks or bdb tests if not installed Dec 2, 2018
optional-requirements.txt Revert "100% threshold optimisation" Feb 2, 2019
requirements.txt Add query score option (#44) Feb 3, 2019

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 An index of the microbial ENA/SRA (Dec 2016) can be queried at

You can read more in the publication.


See: for install instructions.


Quickstart available at


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:

if you use BIGSI in your work.

You can’t perform that action at this time.