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

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 (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 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.