Compact and evenly distributed k-mer binning for genomic sequences.

ABSTRACT:

Motivation

The processing of k-mers (subsequences of length k) is at the foundation of many sequence processing algorithms in bioinformatics, including k-mer counting for genome size estimation, genome assembly, and taxonomic classification for metagenomics. Minimizers-ordered m-mers where m < k-are often used to group k-mers into bins as a first step in such processing. However, minimizers are known to generate bins of very different sizes, which can pose challenges for distributed and parallel processing, as well as generally increase memory requirements. Furthermore, although various minimizer orderings have been proposed, their practical value for improving tool efficiency has not yet been fully explored.

Results

We present Discount, a distributed k-mer counting tool bas

SUBMITTER: Nystrom-Persson J 

PROVIDER: S-EPMC8428581 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature