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

Reumerman, Richard A and Tucker, Nicholas P and Herron, Paul R and Hoskisson, Paul A 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: International Journal of General and Molecular Microbiology, 104 (3). pp. 431-434. ISSN 0003-6072 (https://doi.org/10.1007/s10482-013-9953-x)

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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.

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