Automated analysis and visualization generation of the LD12 genomes and the freshwater genomes comparison paper.

• All code written by Lucas Sinclair.

The published paper for which this pipeline was made can be found here:

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2015260a.html

The code is documented with many docstrings, in addition here is overview of what happens in the analysis:

The command line tool supports a few optional arguments:

• e_value : Minimum e-value in similarity search. Defaults to 0.0001.
• mcl_factor : The MCL clustering factor. Defaults to 1.5.
• seq_type : Either nucl or prot. Defaults to prot.
• num_threads : Number of threads to use. Default to the number of cores on the current machine.
• min_identity : Minimum identity in similarity search. Defaults to 0.97.
• min_coverage : Minimum query coverage in similarity search. Defaults to 0.97.