ArticleNature microbiology2024
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Expanded detection of canine enteric viruses in UK dogs with diarrhoea.Microbial genomics · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- Review
- The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.Nature communications · 2026Article
- Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential ofbioRxiv : the preprint server for biology · 2026Article
- Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.Nature communications · 2026Article
- Diversity and ecological potential of sediment viruses from Chinese continental shelf seas.NPJ biofilms and microbiomes · 2026Article
- A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.bioRxiv : the preprint server for biology · 2026Article
- Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.Science advances · 2026Article
- A satellite in the phage universe: isolation and characterization of six novelFEMS microbes · 2026Article
- Mosquito viromes across England and Wales reveal hidden arbovirus signals and limited ecological structuring.Frontiers in microbiology · 2026Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A novel lineage of large aquatic bacteriophages identified through metagenomics.Archives of virology · 2025Article
- Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.Microbiome · 2025Article
- Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.Virology journal · 2025Article
- ViromeXplore: integrative workflows for complete and reproducible virome characterization.Briefings in bioinformatics · 2025Article
- A prevalent huge phage clade in human and animal gut microbiomes.bioRxiv : the preprint server for biology · 2025Article
- Negativeome characterization and decontamination in early-life virome studies.Nature communications · 2025Article
- Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.bioRxiv : the preprint server for biology · 2025Article
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Abstract
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.
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