Scripts & Programs

More to come! I have a bunch on my GitHub I haven't written docs for. see http://github.com/happykhan

BRIG

The BLAST Ring image Generator (BRIG) is a desktop application I developed for producing circular genome comparison figures. Read more about it here.

The program is freely available at http://brig.sourceforge.net/

BRIG example output image of a simulated draft E. coli O157:H7 genome. The figure show BLAST comparisons of 28 other published (E. coli and Salmonella) genomes against the simulated draft genome.

binCrisp

binCrisp is a Python program I developed that generates figures that shows the distribution of unique spaces sequences from CRISPRs.

The program is still under development and is freely available on GitHub.

Distribution of unique spacer sequences from CRISPRs within a number of E. coli genomes.

SeqFindR

SeqFindr is a Python program that generates figures showing gene presence/absence. The tool was developed by my Beatson-lab colleague, Mitchell Stanton-Cook, and I have been also helping out with its development.

The program is still under development and is freely available here.

"SeqFindR CU fimbriae genes image. 110 E. coli strains were investigated. Order is according to phylogenetic analysis. Black blocks represent gene presence."

EasyFig

EasyFig is a visualisation tool developed by my Beatson-lab colleague Mitchell Sullivan.

From the EasyFig paper: "Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface.

"Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and and Microsoft Windows) from the SourceForge web site."

EasyFig example image: "Comparison of three E. coli with GC content of top genome plotted."