ArticleGenome biology2019
MetaCarvel: linking assembly graph motifs to biological variants.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.bioRxiv : the preprint server for biology · 2026Article
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.Nature methods · 2024Article
- Graph-based self-supervised learning for repeat detection in metagenomic assembly.Genome research · 2024Article
- Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.Bioinformatics (Oxford, England) · 2024Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.bioRxiv : the preprint server for biology · 2024Article
- KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2024Article
- PRAWNS: compact pan-genomic features for whole-genome population genomics.Bioinformatics (Oxford, England) · 2023Article
- KOMB: K-core based de novo characterization of copy number variation in microbiomes.Computational and structural biotechnology journal · 2022Article
- Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads.BMC genomics · 2021Article
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.Frontiers in microbiology · 2021Article
- Whole-Genome Assessment of ClinicalFrontiers in microbiology · 2021Article
- metaFlye: scalable long-read metagenome assembly using repeat graphs.Nature methods · 2020Article
- HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.Genome research · 2020Article
- Expanding the scope and scale of microbiome research.Genome biology · 2019Article
- MetaCarvel: linking assembly graph motifs to biological variants.Genome biology · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains. Previous methods have addressed these issues by smoothing genomic variants. We present a variant-aware metagenomic scaffolder called MetaCarvel, which combines new strategies for repeat detection with graph analytics for the discovery of variants. We show that MetaCarvel can accurately reconstruct genomic segments from complex microbial mixtures and correctly identify and characterize several classes of common genomic variants.
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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.