NGS-SNP - Overview
Citing NGS-SNP
Grant JR, Arantes AS, Liao X, Stothard P (2011) In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 27:2300-2301.
Description
NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms 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 allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A “Model_Annotations” field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species.
NGS-SNP scripts
- annotate_SNPs.pl - used to annotate SNPs identified by the sequencing of genomic DNA or transcripts.
- annotate_INDELs.pl - used to annotate INDELs identified by the sequencing of genomic DNA.
- merge_and_sort_SNP_lists.pl - used to filter, merge, and sort SNP lists annotated using NGS-SNP.
- cDNA_library_entropy.pl - used to choose the best tissues for SNP discovery by mRNA sequencing.
- obtain_reference_chromosomes.pl - used to obtain reference chromosome sequences from Ensembl that can be supplied to SNP discovery tools such as Maq.
- obtain_reference_transcripts.pl - used to obtain reference transcript sequences from Ensembl that can be supplied to SNP discovery tools such as Maq.
- get_genes_in_area.pl - used to obtain information about genes located within or nearby CNVs or other variants supplied as input.
- ncbi_monitor.pl - used to obtain publications related to genome regions supplied as input.
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