SolSNP statistics

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SolSNP specifications


Unique identifier OMICS_00079
Name SolSNP
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License MIT License
Computer skills Advanced
Version 1.11
Stability Stable
Maintained Yes




No version available

SolSNP citations


Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus

PLoS One
PMCID: 4498916
PMID: 26161978
DOI: 10.1371/journal.pone.0130955

[…] AST [] was used for all alignments. Indels and reads mapping to multiple locations were removed from the final alignments. Each alignment was analyzed for single nucleotide polymorphisms (SNPs) using SolSNP ( Only loci that had a minimum coverage of 10X and the base variant was present in greater than 90% of the calls, were included in the final analysis. A […]


Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data

Genome Med
PMCID: 4487561
PMID: 26136847
DOI: 10.1186/s13073-015-0176-9

[…] BWA-MEM [] or NUCmer [], respectively. SNPs and insertion/deletions (indels) can be identified with variant callers including the UnifiedGenotyper method in GATK [, ], SAMtools [], VarScan [], and/or SOLSNP ([]). Called SNPs can then filtered using user-defined thresholds for read depth (default = 3×) and allele frequency proportion (default = 90 %). All called SNPs are then placed into a matrix t […]


Genotyping of Burkholderia mallei from an Outbreak of Glanders in Bahrain Suggests Multiple Introduction Events

PLoS Negl Trop Dis
PMCID: 4177748
PMID: 25255232
DOI: 10.1371/journal.pntd.0003195
call_split See protocol

[…] es from 2004 to seven genomes from the Bahrain outbreak. Using ATCC 23344 genome as a reference, we identified homologous regions using MUMmer , and found single nucleotide polymorphisms (SNPs) using SolSNP (( After eliminating potential paralogs and positions with missing or ambiguous data among isolates, raw reads containing SNPs were aligned to the refer […]


Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing

Cancer Inform
PMCID: 4179624
PMID: 25288881
DOI: 10.4137/CIN.S13779

[…] amples. A number of somatic mutation tools have emerged in the past 2 years, including deepSNV, Strelka, MutationSeq, MutTect, QuadGT (, Seurat, Shimmer and SolSNP (, jointSNVMix, SomaticSniper, VarScan2, and Virmid. Each of them is equipped with unique features and applications. For example, deepSNV was specially d […]


Origin and Evolution of European Community Acquired Methicillin Resistant Staphylococcus aureus

PMCID: 4173770
PMID: 25161186
DOI: 10.1128/mBio.01044-14

[…] the 11819-97 reference genome using the short-read alignment component of the Burrows-Wheeler aligner (), and external genomes were aligned using MUMmer (). Each alignment was analyzed for SNPs using SolSNP ( and excluded all SNPs that did not meet a minimum coverage of 10 or if the variant was present in <90% of the base calls for that position. SNPs identi […]


Phylogeography of Bacillus anthracis in the Country of Georgia Shows Evidence of Population Structuring and Is Dissimilar to Other Regional Genotypes

PLoS One
PMCID: 4105404
PMID: 25047912
DOI: 10.1371/journal.pone.0102651

[…] To identify putative SNPs, homologous genomic regions were identified using MUMmer and aligned to search for SNPs using SolSNP ( We ensured site orthology by eliminating potential paralogs and requiring all genome alignments to include 100 bp flanking each side of the SNP. Furth […]


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