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

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