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Bioinformatics. 2011 Aug 15;27(16):2300-1. doi: 10.1093/bioinformatics/btr372. Epub 2011 Jun 22.

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP.

Author information

1
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada.

Abstract

SUMMARY:

NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons can, for example, identify SNPs that affect conserved residues, or alter residues or genes linked to phenotypes in another species.

AVAILABILITY:

NGS-SNP is available both as a set of scripts and as a virtual machine. The virtual machine consists of a Linux operating system with all the NGS-SNP dependencies pre-installed. The source code and virtual machine are freely available for download at http://stothard.afns.ualberta.ca/downloads/NGS-SNP/.

CONTACT:

stothard@ualberta.ca

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
21697123
PMCID:
PMC3150039
DOI:
10.1093/bioinformatics/btr372
[Indexed for MEDLINE]
Free PMC Article

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