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Protocols

SolSNP specifications

Information


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

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SolSNP citations

 (18)
library_books

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

2015
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 (http://sourceforge.net/projects/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 […]

library_books

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

2015
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 […]

call_split

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

2014
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 ((http://sourceforge.net/projects/solsnp/). After eliminating potential paralogs and positions with missing or ambiguous data among isolates, raw reads containing SNPs were aligned to the refer […]

library_books

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

2014
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 (http://www.iro.umontreal.ca/~csuros/quadgt), Seurat, Shimmer and SolSNP (http://source-forge.net/projects/solsnp), jointSNVMix, SomaticSniper, VarScan2, and Virmid. Each of them is equipped with unique features and applications. For example, deepSNV was specially d […]

library_books

Origin and Evolution of European Community Acquired Methicillin Resistant Staphylococcus aureus

2014
MBio
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 (http://sourceforge.net/projects/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 […]

library_books

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

2014
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 (http://sourceforge.net/projects/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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