KmerKeys: a web resource for searching indexed genome assemblies and variants.

ABSTRACT: K-mers are short DNA sequences that are used for genome sequence analysis. Applications that use k-mers include genome assembly and alignment. However, the wider bioinformatic use of these short sequences has challenges related to the massive scale of genomic sequence data. A single human genome assembly has billions of k-mers. As a result, the computational requirements for analyzing k-mer information is enormous, particularly when involving complete genome assemblies. To address these issues, we developed a new indexing data structure based on a hash table tuned for the lookup of short sequence keys. This web application, referred to as KmerKeys, provides performant, rapid query speeds for cloud computation on genome assemblies. We enable fuzzy as well as exact sequence searches of assem

SUBMITTER: Pavlichin DS 

PROVIDER: S-EPMC9252721 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature