Fairy: fast approximate coverage for multi-sample metagenomic binning.

ABSTRACT:

Background

Metagenomic binning, the clustering of assembled contigs that belong to the same genome, is a crucial step for recovering metagenome-assembled genomes (MAGs). Contigs are linked by exploiting consistent signatures along a genome, such as read coverage patterns. Using coverage from multiple samples leads to higher-quality MAGs; however, standard pipelines require all-to-all read alignments for multiple samples to compute coverage, becoming a key computational bottleneck.

Results

We present fairy ( https://github.com/bluenote-1577/fairy ), an approximate coverage calculation method for metagenomic binning. Fairy is a fast k-mer-based alignment-free method. For multi-sample binning, fairy can be >250× faster than read alignment and accurate enough for binning. Fairy

SUBMITTER: Shaw J 

PROVIDER: S-EPMC11323348 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature