Metagenomic functional profiling: to sketch or not to sketch?

ABSTRACT:

Motivation

Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.

Results

We show how pieces of the sourmash software (and the r

SUBMITTER: Hera MR 

PROVIDER: S-EPMC11373326 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature