ArticleGenome biology2024
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities.Entropy (Basel, Switzerland) · 2025Article
- Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.Functional & integrative genomics · 2025Review
- Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.Bioinformatics (Oxford, England) · 2025Article
- Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.Microorganisms · 2024Review
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundIn the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.
resultsHere, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.
conclusionsOur work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.