ld12 version 1.0.1
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:
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
mcl_factor: The MCL clustering factor. Defaults to
prot. Defaults to
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
min_coverage: Minimum query coverage in similarity search. Defaults to