When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes
bioinformaticssnpphylogeneticsmicrobial-genomicsk-mer
Abstraction: Alignment-free k-mer SNP discovery tool for hundreds of microbial genomes
Key points:
- kSNP v2 finds SNPs and builds phylogenies across hundreds of bacterial/viral genomes without a reference genome or multiple sequence alignment
- Uses k-mer analysis (typically k=19-21 for bacteria, 13-15 for viruses); includes Kchooser script to select optimal k
- Analyzed 212 Salmonella genomes in 6.9 hours on a 48 GB/12-CPU node; handles raw unassembled reads
- Builds Maximum Likelihood, Neighbor Joining, and parsimony trees from all SNPs, core SNPs, or user-specified fraction
- Annotates SNPs with GenBank gene/protein/amino-acid data downloaded automatically from NCBI
- Cannot distinguish sequencing errors from true SNPs; does not detect indels
Connections: Ksnp · Ncbi · Snp Discovery · Phylogenetics · K Mer Analysis
Source: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081760