NGS-SNP statistics

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NGS-SNP specifications

Information


Unique identifier OMICS_00177
Name NGS-SNP
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Versioning


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Maintainer


  • person_outline Paul Stothard <>

Publication for NGS-SNP

NGS-SNP in pipelines

 (2)
2016
PMCID: 4753642
PMID: 26876963
DOI: 10.1186/s13073-016-0273-4

[…] and single nucleotide variants (snvs) were called by gatk’s unifiedgenotyper, both using dbsnp version 137 as the background single nucleotide polymorphism (snp) set. snv annotations were done using ngs-snp []. indels were annotated using the variant effect predictor []., snvs and indels were then compared against the precompiled list found in 18 inbred strains from the mouse genome project []. […]

2014
PMCID: 4190571
PMID: 25296911
DOI: 10.1038/srep06556

[…] the results were then subject to additional filtering to remove snps with low quality value and low read coverage. functional classification and annotation of the predicted snps were performed using ngs-snp tool. databases ensembl (release 63), entrezgene, and gene ontology were used as reference for annotation. several fields of other information, such as descriptions of the influenced […]


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NGS-SNP in publications

 (23)
PMCID: 5889553
PMID: 29625549
DOI: 10.1186/s12711-018-0387-9

[…] for the four traits (2025 for each trait, with 245 shared between at least two traits)., the imputed whole-genome variants were annotated based on the sscrofa 10.2 assembly of the swine genome using ngs-snp []. all variants were then defined as belonging to one of three broad categories, as suggested by macleod et al. []. the first category, which will be referred to as “nsc”, comprised variants […]

PMCID: 5885354
PMID: 29618315
DOI: 10.1186/s12864-018-4617-x

[…] of the annotations were obtained from ensembl release 77 [] except for the 3prime untranslated region (utr), 5prime utr, synonymous, missense deleterious and missense tolerated which came from the ngs-snp pipeline []. mirna predicted target sites came from microcosm []. dna methylated regions came from the study by su j et al. []. long noncoding rna (lncrna) and antisense rna (asrna) […]

PMCID: 5609075
PMID: 28934948
DOI: 10.1186/s12711-017-0347-9

[…] approximately two million sequence variants in gene coding regions and variants that were 5000 bp up- and down-stream of genes were imputed. annotations for the sequence variants were collated using ngs-snp []. after filtering out variants with a minor allele frequency (maf) lower than 0.0002 and variants in complete ld, this dataset (seq) contained 994,019 variants, including 45,026 […]

PMCID: 5499214
PMID: 28683716
DOI: 10.1186/s12711-017-0331-4

[…] conversion files (chain file format) were downloaded from the ucsc (university of california, santa cruz) database [] on 29 february 2016. annotations for the sequence variants were collated using ngs-snp []. the bovine quantitative trait loci (qtl) annotation file was downloaded from the animal qtl database (animal qtldb) [] on 17 may 2016., the human and mouse enhancer regions from vista, […]

PMCID: 4992138
PMID: 27534441
DOI: 10.1038/ncomms12444

[…] of snvs. the overlapping sites were removed resulting in a final list of unique enu snvs for each g1. these snvs were then functionally annotated (for example, missense, intronic and so on) using ngs-snp. all high-confidence mutations are available on mousebook. for individual mutant lines snvs were confirmed by sanger sequencing of affected mice., phenotype data was initially captured […]


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NGS-SNP institution(s)
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
NGS-SNP funding source(s)
Supported by Alberta Livestock and Meat Agency and the Natural Sciences and Engineering Research Council of Canada.

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