SolSNP statistics

info info

Citations per year

info

Popular tool citations

chevron_left SNP detection chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

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

Download


download.png
sourceforge.png

Versioning


No version available

SolSNP citations

 (16)
library_books

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

2015
PMCID: 4498916
PMID: 26161978
DOI: 10.1371/journal.pone.0130955

[…] [] 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. […]

library_books

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

2015
PMCID: 4487561
PMID: 26136847
DOI: 10.1186/s13073-015-0176-9

[…] [] 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 […]

library_books

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

2014
PMCID: 4177748
PMID: 25255232
DOI: 10.1371/journal.pntd.0003195

[…] 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 […]

library_books

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

2014
PMCID: 4179624
PMID: 25288881
DOI: 10.4137/CIN.S13779

[…] 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 […]

library_books

Origin and Evolution of European Community Acquired Methicillin Resistant Staphylococcus aureus

2014
PMCID: 4173770
PMID: 25161186
DOI: 10.1128/mBio.01044-14

[…] 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 […]

library_books

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

2014
PMCID: 4105404
PMID: 25047912
DOI: 10.1371/journal.pone.0102651

[…] into genbank (prjna224563, prjna224558, and prjna224562, respectively) ()., 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. […]


Want to access the full list of citations?

SolSNP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SolSNP