Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes.

Reumerman, Richard, Tucker, Nicholas, Herron, Paul, Hoskisson, Paul and Sangal, Vartul (2013) Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes. Antonie van Leeuwenhoek, 104 (3). pp. 431-4. ISSN 1572-9699

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Abstract

Next generation sequencing (NGS) has been widely used to study genomic variation in a variety of prokaryotes. Single nucleotide polymorphisms (SNPs) resulting from genomic comparisons need to be annotated for their functional impact on the coding sequences. We have developed a program, TRAMS, for functional annotation of genomic SNPs which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. TRAMS needs a tab delimited text file containing SNP locations, reference nucleotide and SNPs in variant strains along with a reference genome sequence in GenBank or EMBL format. SNPs are annotated as synonymous, nonsynonymous or nonsense. Nonsynonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in multiple overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms within a codon are combined before annotation. We have also developed a workflow for Galaxy, a highly used tool for analysing NGS data, to map short reads to a reference genome and extract and annotate the SNPs. TRAMS is a simple program for rapid and accurate annotation of SNPs that will be very useful for microbiologists in analysing genomic diversity in microbial populations.

Item Type:	Article
Subjects:	C500 Microbiology
Department:	Faculties > Health and Life Sciences > Applied Sciences
Depositing User:	Vartul Sangal
Date Deposited:	08 Nov 2013 15:38
Last Modified:	12 Oct 2019 18:28
URI:	http://nrl.northumbria.ac.uk/id/eprint/14521

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