title: In-depth annotation of SNPs arising from resequencing projects using NGS-SNP.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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/.
  
  
  BACKGROUND
  stothard@ualberta.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Grant
authors.forename: Adriano S
authors.initials: AS
authors.lastname: Arantes
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Liao
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
mesh_terms: D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software