ArticleGenome biology2020
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Landscape of Genetic Content in the Gut and Oral Human Microbiome.Cell host & microbe · 2019Pooled it
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- A holistic genome dataset of bacteria and archaea of mangrove sediments.GigaScience · 2025Article
- ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.Frontiers in microbiology · 2025Article
- Metagenomic assemblies tend to break around antibiotic resistance genes.BMC genomics · 2024Article
- Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater.Frontiers in microbiology · 2024Article
- Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.ISME communications · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Capturing variation in metagenomic assembly graphs with MetaCortex.Bioinformatics (Oxford, England) · 2023Article
- Ten simple rules and a template for creating workflows-as-applications.PLoS computational biology · 2022Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments.Nature communications · 2022Article
- Article
- Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling.Frontiers in microbiology · 2022Article
- KOMB: K-core based de novo characterization of copy number variation in microbiomes.Computational and structural biotechnology journal · 2022Article
- Article
- STRONG: metagenomics strain resolution on assembly graphs.Genome biology · 2021Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementation is available at https://github.com/spacegraphcats/spacegraphcats under the 3-Clause BSD License.
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