kSNP pipeline

kSNP specifications

Information


Unique identifier OMICS_08467
Name kSNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of the paths to the original genome files.
Operating system Unix/Linux, Mac OS
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 3.0.21
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Barry G. Hall <>

Publications for kSNP

kSNP IN pipelines

 (2)
2017
PMCID: 5398294
PMID: 28379509
DOI: 10.1093/gbe/evx062

[…] performing a blastx search in the ncbi genbank nr database and using the predicted protein of the query sequences under the thresholds of the highest bit-score and e-value (≤ 1e-03)., we constructed ksnp trees, genome-wide trees, and pan-genome trees using whole-genome sequence data of 106 s. suis and other streptococcus spp. strains (fig. 1 and supplementary figs. s1–s3, supplementary material […]

2016
PMCID: 5156309
PMID: 27965456
DOI: 10.1128/mBio.02093-16

[…] 2.1 (39) and plasmidfinder 1.3 (65). additional novel plasmid replicons from the present study were included in the analysis as well., a phylogenetic tree was inferred from snps identified by ksnp v 3.0 (30) by using a k-mer length of 19 nucleotides and a requirement that at least 80% of the genomes (i.e., 303 genomes) have a nucleotide at a given snp position in order for the snp […]

kSNP institution(s)
Computations/Global Security, Lawrence Livermore National Laboratory, Livermore, CA, USA; Bellingham Research Institute, Bellingham, WA, USA
kSNP funding source(s)
Supported under internal funding at LLNL.

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