When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

PLoS One. 2013 Dec 9;8(12):e81760. doi: 10.1371/journal.pone.0081760. eCollection 2013.

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.

MeSH terms

  • Algorithms
  • Computational Biology*
  • Databases, Nucleic Acid
  • Escherichia coli / classification
  • Escherichia coli / genetics*
  • Escherichia coli / pathogenicity
  • Genome, Bacterial*
  • Humans
  • Molecular Sequence Annotation
  • Phylogeny*
  • Polymorphism, Single Nucleotide*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Shigella / classification
  • Shigella / genetics*
  • Software*

Grant support

This work was supported by the US Department of Homeland Security Science and Technology Directorate via awards HSHQPM-10-X-00078 P00001 and HSHQPM-10-X-00099 P00002. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.