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README.md

ld12 version 1.0.1

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

Publication

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

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

Flowchart

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

Flowchart

Optional arguments

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.

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Analysis of the LD12 genomes and the freshwater genomes for the "Tuning fresh" paper

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