biostudies-literatureShaw JNatural Sciences and Engineering Research Council of Canada151https://www.ebi.ac.uk/biostudies/studies/S-EPMC11323348biostudies-literatureUnknown12(1)<h4>Background</h4>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.<h4>Results</h4>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 MicrobiomeFairy: fast approximate coverage for multi-sample metagenomic binning.PMC11323348CGS-DRGPIN-2022-309 03074Yu YWShaw JfalseFairy: fast approximate coverage for multi-sample metagenomic binning.<h4>Background</h4>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.<h4>Results</h4>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 2024-01-01T00:00:00Z2024 Aug2025-05-18T12:13:03.576Z2025-04-05T10:09:15.166ZS-EPMC113233483914360910.1186/s40168-024-01861-6