SolSNP statistics

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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 in pipelines

 (4)
2013
PMCID: 3870262
PMID: 24345742
DOI: 10.1128/mBio.00377-13

[…] published st131 reference genome (strain na114; genbank accession no. cp002797) () using the short-read alignment component of the burrows-wheeler aligner. each alignment was analyzed for snps using solsnp, a java-based dna variant-calling tool for next-generation sequencing alignment data. solsnp uses a modified kolmogorov-smirnov statistic and data filtering to call variants on high-coverage, […]

2012
PMCID: 3414016
PMID: 22840345
DOI: 10.3201/eid1808.111343

[…] data filtering were performed with samtools 0.1.12a () by using an in-house java script that filtered out results, providing <10× coverage. for in-house genomes, snp calls were then made by using solsnp version 1.1 with the following alignment limits: minimum coverage of 20, minimum mapping qualities of 20, and a filter call of 0.95. mummer 3.20 () was used to determine snp calls in public […]

2012
PMCID: 3507928
PMID: 23209631
DOI: 10.1371/journal.pone.0049989

[…] (bwa) alignment tool . reads containing insertions or deletions, and those mapping to multiple locations in the reference were removed from the final alignments., snp detection was conducted using solsnp (http://solsnp.sourceforge.net/), a publically available in-house developed tool. snps were excluded if they did not meet a minimum coverage of 10× and if the variant was present in less […]

2011
PMCID: 3233577
PMID: 22163313
DOI: 10.1371/journal.pone.0028550

[…] aligner ., reads containing insertions or deletions, and those mapping to multiple locations in the reference were removed from the final alignments. each alignment was analyzed for snps using solsnp (http://sourceforge.net/projects/solsnp/). snps were excluded if they did not meet a minimum coverage of 10× and if the variant was present in less than 90% of the base calls […]


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SolSNP in publications

 (15)
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. […]

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 […]

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 […]

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 […]

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 […]


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