ArticleGenome biology2021
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
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- Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.Bioinformatics (Oxford, England) · 2026Article
- Detecting "invisible"ISME communications · 2026Article
- Detecting poliovirus sequences in the sequence read archive database using bioinformatics tools.Frontiers in bioinformatics · 2026Article
- A replication-competent deltavirus from the marsupial fat-tailed dunnartThe Journal of general virology · 2026Article
- Benchmarking of human read removal strategies for viral and microbial metagenomics.Cell reports methods · 2025Article
- Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.Journal of translational medicine · 2025Article
- Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.Nutrients · 2025Article
- Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.mSystems · 2025Article
- The hidden life ofApplied and environmental microbiology · 2025Article
- The GSA Family in 2025: A Broadened Sharing Platform for Multi-omics and Multimodal Data.Genomics, proteomics & bioinformatics · 2025Article
- Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.bioRxiv : the preprint server for biology · 2025Article
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- HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries.Bioinformatics (Oxford, England) · 2025Article
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- Draft Genome of Naganishia uzbekistanensis from a Clinical Pulmonary Infection.Mycopathologia · 2025Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms.
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