This is a set of basic scripts for analyzing genomic data, particularly rearrangements.

Scripts do not include novel algorthms or applications, but are developed to mediate analysis workflows using other freely-available software as described. Everything is written in Perl, though probably not that well. All scripts include brief documentation, accessible by passing no parameters. Separate versions of the workflows are available in these directories:

1. Weigand_JBact2007/ -- versions used for Weigand et al. 2017.
2. Current/ -- copy of active versions in use with subsequent projects.
3. Example_data/ -- small dataset of genomes for testing

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Included Analysis Workflows:

As described in Weigand et al. 2017 :

1. WORKFLOW-REARRANGEMENTS.md: Characterize genome rearrangements in complete assemblies.
2. WORKFLOW-IS481.md: Match variable IS481 insertions in a set of genomes.

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Disclaimer

The contents of this repository are intended for research purposes only and come with no guarantees of their performance.