ArticleNature methods2025
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.Briefings in bioinformatics · 2026Article
- Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.Nature microbiology · 2026Article
- Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.Nature communications · 2026Article
- Unbinned contigs expand known diversity in the global microbiome.Nature microbiology · 2026Article
- GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes.Nucleic acids research · 2026Article
- Article
- Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly.iMeta · 2025Article
- Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.Nature microbiology · 2025Article
- GlobDB: a comprehensive species-dereplicated microbial genome resource.Bioinformatics advances · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
The recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low-abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm that substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritized, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.
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Registered trials
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