ArticleNature communications2024
BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
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- The Role of Phytoplankton and Sediment Microbial Community on Sr, U, Pu, and Am Behavior in Freshwater Lake Dryazlo.Biology · 2026Article
- Spatially resolved denitrification coupled with methane and arsenite oxidation at the millimeter-scale straw-soil interface.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.Microbiome · 2026Article
- The core microbiome of the AMF hyphosphere: mineralization mechanisms of key soil mineral elements.Mycorrhiza · 2026Review
- An integrated culturomic and genomic database and analysis platform for methanogenic archaea.Database : the journal of biological databases and curation · 2026Article
- High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.The ISME journal · 2026Article
- Quorum-sensing microbial dark matter enables core functions in wastewater microbiomes.ISME communications · 2026Article
- Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.Scientific data · 2025Article
- Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.Scientific reports · 2025Article
- Diversity of Groundwater Microbial Communities near Sludge Repositories with Different Types and Levels of Pollution.Life (Basel, Switzerland) · 2025Article
- Microbial necromass carbon enhances arsenic methylation in paddy soils.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The potential of wastewater monitoring as a novel surveillance tool for early warning ofEmerging microbes & infections · 2025Article
- Gut microbiota-mediated conversion of mangiferin to norathyriol alters short chain fatty acid and urate metabolism.Gut microbes · 2025Article
- Evaluation of metagenome binning: advances and challenges.Briefings in bioinformatics · 2025Article
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Authors and funding
25 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.
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