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 references from a given collection that are likely to contain a query nucleotide sequence - is relevant for many important tasks in Computational Biology, such as metagenomics and pan-genome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resourceefficient solution to this problem is of utmost importance. The reference collection should therefore be pre-processed into an index for fast queries. This poses the threefold challenge of designing an index that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe how recent advancements in associative, order-preserving, k-mer diction

SUBMITTER: Fan J 

PROVIDER: S-EPMC10197524 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature