ArticleNucleic acids research2012
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 289 papers.
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Who cites it
289 citing papers in PubMed.
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.Communications biology · 2026Article
- Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.Interdisciplinary sciences, computational life sciences · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- Bioremediation and optimization of selenate reduction by a novel Bacillus cabrialesii strain (Se1) producing red selenium nanoparticles with potential antibacterial activity.BMC microbiology · 2025Article
- Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.mSystems · 2025Article
- Targeted protein evolution in the gut microbiome by diversity-generating retroelements.Science (New York, N.Y.) · 2025Article
- Review
- Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.Functional & integrative genomics · 2025Review
- Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.Osong public health and research perspectives · 2025Article
- Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- The mycobiome in human cancer: analytical challenges, molecular mechanisms, and therapeutic implications.Molecular cancer · 2025Review
- Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.PeerJ · 2025Article
- Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.Frontiers in microbiology · 2025Review
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.Briefings in bioinformatics · 2024Article
- Targeted protein evolution in the gut microbiome by diversity-generating retroelements.bioRxiv : the preprint server for biology · 2024Article
- A Comparative Study of Microbial Communities, Biogenic Amines, and Volatile Profiles in the Brewing Process of Rice Wines with Hongqu and Xiaoqu as Fermentation Starters.Foods (Basel, Switzerland) · 2024Article
229 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An important step in 'metagenomics' analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines use a single-genome assembler with carefully optimized parameters. A limitation of a single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species are likely misidentified as repeats in a single genome, resulting in a number of small fragmented scaffolds. We extended a single-genome assembler for short reads, known as 'Velvet', to metagenome assembly, which we called 'MetaVelvet', for mixed short reads of multiple species. Our fundamental concept was to first decompose a de Bruijn graph constructed from mixed short reads into individual sub-graphs, and second, to build scaffolds based on each decomposed de Bruijn sub-graph as an isolate species genome. We made use of two features, the coverage (abundance) difference and graph connectivity, for the decomposition of the de Bruijn graph. For simulated datasets, MetaVelvet succeeded in generating significantly higher N50 scores than any single-genome assemblers. MetaVelvet also reconstructed relatively low-coverage genome sequences as scaffolds. On real datasets of human gut microbial read data, MetaVelvet produced longer scaffolds and increased the number of predicted genes.
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Registered trials
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.