ArticlePloS one2013
When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 150 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
150 citing papers in PubMed, 1 synthesis or guideline pooled it, 258 citations in OpenAlex.
- Maast: genotyping thousands of microbial strains efficiently.Genome biology · 2023Pooled it
- Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh.EBioMedicine · 2016Trial
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Whole genome sequencing-based characterization of Escherichia coli isolated from raw beef in selected butcher shops in Addis Ababa and Burayu, Ethiopia.Scientific reports · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
- Phylogeographic clustering ofApplied and environmental microbiology · 2026Article
- Comparative genomic analysis reveals distinct population structure in Legionella anisa.FEMS microbiology letters · 2026Article
- Genetic Determinants Associated With the Biofilm Formation Impairment in Pseudomonas aeruginosa Clinical Isolates.MicrobiologyOpen · 2025Article
- Genome-wide identification of essential genes in the invasive Streptococcus anginosus strain.Scientific reports · 2025Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Genomic profiling of pediococcus acidilactici BCB1H and identification of its key features for Biotechnological innovation, food technology and medicine.Scientific reports · 2025Article
- An alignment- and reference-free strategy usingMycology · 2025Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.G3 (Bethesda, Md.) · 2024Article
- Genome sequence-based species classification ofMicrobiology spectrum · 2024Article
- Building Phylogenetic Trees From Genome Sequences With kSNP4.Molecular biology and evolution · 2023Article
- MIST: A microbial identification and source tracking system for next-generation sequencing data.iMeta · 2023Article
90 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Effective use of rapid and inexpensive whole genome sequencing for microbes requires fast, memory efficient bioinformatics tools for sequence comparison. The kSNP v2 software finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation; better scaling for draft genomes available as assembled contigs or raw, unassembled reads; a tool to identify the optimal value of k; distribution of packages of executables for Linux and Mac OS X for ease of installation and user-friendly use; and a detailed User Guide. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a single reference genome. Most target sets with hundreds of genomes complete in minutes to hours. SNP phylogenies are built by maximum likelihood, parsimony, and distance, based on all SNPs, only core SNPs, or SNPs present in some intermediate user-specified fraction of targets. The SNP-based trees that result are consistent with known taxonomy. kSNP v2 can handle many gigabases of sequence in a single run, and if one or more annotated genomes are included in the target set, SNPs are annotated with protein coding and other information (UTRs, etc.) from Genbank file(s). We demonstrate application of kSNP v2 on sets of viral and bacterial genomes, and discuss in detail analysis of a set of 68 finished E. coli and Shigella genomes and a set of the same genomes to which have been added 47 assemblies and four "raw read" genomes of H104:H4 strains from the recent European E. coli outbreak that resulted in both bloody diarrhea and hemolytic uremic syndrome (HUS), and caused at least 50 deaths.
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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.