ArticleGenome biology2019
Mash Screen: high-throughput sequence containment estimation for genome discovery.
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 193 papers.
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Who cites it
193 citing papers in PubMed.
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- DNA modifications of Durham Collection phages and promiscuity of GmrSD-family Type IV restriction enzyme BrxU.Applied and environmental microbiology · 2026Article
- Sequencing the genome ofMicrobiology resource announcements · 2026Article
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- A Malectin-Like Receptor Kinase and Bacterial Motility Shape Tissue-Specific Maize-Xanthomonas vasicola Interactions.Molecular plant pathology · 2026Article
- Genome assemblies of two bumble bee species: Bombus sonorus and Bombus vosnesenskii.The Journal of heredity · 2026Article
- nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.Bioinformatics (Oxford, England) · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Allelic variation of Avr genes in highly virulent strains explains severe wheat stem rust epidemics.Nature communications · 2026Article
- Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets.Molecular diversity · 2026Article
- Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.Microbial genomics · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- Two Vibrio species co-colonize a morphologically complex symbiotic light organ.The ISME journal · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
133 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery. Using this tool, we provide containment estimates for every NCBI RefSeq genome within every SRA metagenome and demonstrate the identification of a novel polyomavirus species from a public metagenome.
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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.