When a researcher has a new genome sequence, one of the first things they want to identify is the closest relatives of their genome. BV-BRC provides a service that allows researchers to do this using Mash/MinHash[1]. Mash reduces large sequences and sequence-sets to small, representative sketches, from which global mutation distances can be rapidly estimated. The MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections.
This module contains the service code that implements the BV-BRC Similar Genome Finder service.
It provides utilities for maintaining a minhash database of the collected BV-BRC genomes (both bacterial and viral) and a JSONRPC-based synchronous lookup service. The BV-BRC API uses this service to implement the similar genome finder service.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
This service is run as a sychronous service via the KBase JSONRPC service mechanism. As such, the API for the service is defined in the Minhash.spec file.
Ondov BD, Treangen TJ, Melsted P et al. Mash: fast genome and metagenome distance estimation using MinHash, Genome biology 2016;17:132.