Fulgor: a fast and compact k-mer index for large-scale matching and color queries.

ABSTRACT: The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted i

SUBMITTER: Fan J 

PROVIDER: S-EPMC10810250 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature