PhasomeIt – identification and classification of SSR-mediated PV loci

PhasomeIt is a software tool for identifying and grouping phase variable loci in a group of genomes. It identifies PV loci based on the presence of short simple sequence repeats (SSRs) (found using Bossref) and then uses BLAST to group the loci present in all genomes into homology groups. It will then output this data into HTML format (see here for an example output for Campylobacter). PhasomeIt is written in Python (version 3.3.5 or above) but requires Bossref to function and the BLAST+ suite installed to run from the default path. The BioPython and NatSort python packages are also required.

PhasomeIt is now supported via GitHub and the latest version can be found there.

Bossref for Windows and Linux is included in the download, but requires a 64-bit Intel-compatible processor. Note that when running on Linux you may need to set the executable permission bit on the ‘bossref’ file included in the download for it to function.

Citation

Aidley et al (2018) PhasomeIt: an ‘omics’ approach to cataloguing the potential breadth of phase variation in the genus Campylobacter https://doi.org/10.1099/mgen.0.000228

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