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

TRAMS (Tool for Rapid Annotation of Microbial SNPs) is a program 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 only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. TRAMS annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation.

We have also developed a workflow for use in Galaxy 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.

Availability: TRAMS is available here to download as Python script and single file executable for WINDOWS and also in the Galaxy tool shed (http://toolshed.g2.bx.psu.edu/view/rreumerman/snptools).

 

Please cite

Reumerman, R. A., Tucker, N. P., Herron, P. R., Hoskisson, P. A., & Sangal, V. (2013). Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes. Antonie van Leeuwenhoek, 104, 431-434. doi:10.1007/s10482-013-9953-x

The full published manuscript is available

http://link.springer.com/article/10.1007%2Fs10482-013-9953-x

UPDATED 24th September 2013 see Changelog.txt

==[Version1.0.2]==

130923:Fixed issue where program crashed on absence of certain features in genbank file.

==[Version1.0.1]==

130919:Fixed issue where'Gene'and'Source' were not recognized as'gene'and'source'.

130919:Fixed issue where features' strands were mysteriously no longer recognized if on +1 strand.