BItsliced Genomic Signature Index [bigsi]

BItsliced Genomic Signature Index [BIGSI] Docs

Welcome to the BIGSI documentation. You'll find comprehensive guides and documentation to help you start working with BIGSI as quickly as possible.

BIGSIs–BItsliced Genomic Signature Indexes–allow for efficient indexing and search in very large collections of WGS data, in particular bacterial or viral data sets WGS data sets. BIGSI can index and query raw, or assembled data.

A prebuilt index is available for download at http://ftp.ebi.ac.uk/pub/software/bigsi/nat_biotech_2018/all-microbial-index-v0.3 or a hosted demo is available here http://www.bigsi.io/.

Please cite our paper if you use this tool in your research:
'Ultra-fast search of all deposited bacterial and viral genomic data' http://dx.doi.org/10.1038/s41587-018-0010-1

Get Started    Guides

What is BIGSI?

BIGSI indexes a set of N bloom filters by position in the bloom filter. Each bloom filter must be constructed with the same parameters (m, η), where m is the bloom filter’s length in bits and η is the number of hash functions applied to each k-mer. The same hash functions must also be used to construct each bloom filter. To construct a BIGSI, the N bloom filters are column-wise concatenate into a matrix. The row index and row bit-vectors are then inserted into a hash table or key-value store as key-value pairs so that row lookups can be done in O(1) time. This set of key-value pairs can be stored on disk, in memory or distributed across several machines. To insert a new bloom filter we simply append it as a column to the existing bitmatrix.
To query the BIGSI for a k-mer we hash the k-mer η times, look up the resulting keys in the key-value store, and take the bit-wise AND of the resulting bit-vectors.

In the figure we can see BIGSI encoding compared with naïve approach. a) BIGSI step 1: each input dataset (could be raw sequence data (FASTQ format) or assembly) is converted to a non-redundant list of kmers (with an optional denoising step to remove sequencing errors, detailed in Methods). A fixed set of η hash functions (h_1,h_2,…) is applied to each k-mer (η =3 in this figure), giving a tuple of positions which are all be set to 1 in a bit-vector (a Bloom Filter). b) BIGSI step 2. Each dataset is stored as a fixed length bloom filter, as a column in a rectangular matrix. To query the BIGSI for k-mer AAT, the η hash functions are applied to the query k-mer, returning η rows to be checked (namely 3,7,5 here). All columns (datasets) that have 1 in all of those η rows contain the query k-mer: these rows that are checked are called “bitslices”. Adding a new dataset requires just adding a new column. c) Naïve encoding for contrast. A complete list of all k-mers in all datasets form the rows of a large matrix, and columns are datasets. For any given k-mer, entries are set to one for datasets containing that k-mer. When a new dataset is added, the matrix grows vertically (new k-mers added) and horizontally (new column for new dataset).

You can read more about is in our publication:

'Ultra-fast search of all deposited bacterial and viral genomic data' http://dx.doi.org/10.1038/s41587-018-0010-1

Preprint is available here:

https://www.biorxiv.org/content/early/2017/12/15/234955

and get started by reading the docs: https://bigsi.readme.io/docs