ArticlePeerJ2017
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
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- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- Genomics reveal Staphylococcus aureus persists during long-term urinary catheterization despite antimicrobial therapy and catheter exchanges.Nature communications · 2026Article
- Genomic Characterization of Pan-Drug Resistant Klebsiella pneumoniae KPNW Isolated From UTI Patient in Bangladesh.MicrobiologyOpen · 2025Article
- Whole-genome sequencing surveillance of vancomycin-resistantInfection control and hospital epidemiology · 2025Article
- A network analysis of carbapenem-resistant Klebsiella pneumoniae among healthcare facilities.Scientific reports · 2025Observational
- The Clinical and Molecular Characteristics of Community-AssociatedOpen forum infectious diseases · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- [Real-time rectal swab Xpert Carba-R assay for early warning of CRO bloodstream infection in patients undergoing hematopoietic stem cell transplant: a clinical feasibility study].Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi · 2024Article
- Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis.Scientific reports · 2023Article
- Article
- Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Article
- Article
- VirStrain: a strain identification tool for RNA viruses.Genome biology · 2022Article
- Identification of Antimicrobial Compounds in TwoFrontiers in microbiology · 2022Article
- Identification of isolated or mixed strains from long reads: a challenge met onMicrobial genomics · 2021Article
- Genomic Sequence Analysis of Methicillin- and Carbapenem-Resistant Bacteria Isolated from Raw Sewage.Microbiology spectrum · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees.
resultsA tool named StrainSeeker was developed that constructs a list of specific
conclusionStrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker's web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.
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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.