$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Chen, LinXing; Banfield, Jillian F.

doi:10.1038/s41564-023-01598-2

$$\mathrm{COBRA}$$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Journal Article · Mon Feb 05 23:00:00 EST 2024 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-023-01598-2· OSTI ID:2335317

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University of California, Berkeley, CA (United States)
University of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Natural Sciences and Engineering Research Council of Canada (NSERC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2335317

Journal Information:: Nature Microbiology, Journal Name: Nature Microbiology Journal Issue: 3 Vol. 9; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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54 ENVIRONMENTAL SCIENCES
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genome assembly algorithms
metagenomics
microbial ecology

$$\mathrm{COBRA}$$ improves the completeness and contiguity of viral genomes assembled from metagenomes

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