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#Kvasir

Join the chat at https://gitter.im/kescobo/kvasir

Dependencies:

  • Python 2.7
  • MongoDB
    • pymongo
  • BioPython
  • BLAST+ CLI

Identification of horizontal gene transfer between sequenced microbial genomes

Kvasir takes as the input a folder containing genomes in genbank format. The protein coding genes from these genomes are loaded into a database, and blasted against each other.

Usage

Change the values in settings.py to point at your input folder, output folder, and the name you want for your database.

Launch a local mongod instance:

$ mongod --dbpath path/to/db

Run functions in run.py. Eventually, this will get more streamlined, for now...

Python 2.7.11 (default, Dec 14 2015, 10:44:13)
[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import run
>>> run.import_data()
>>> run.blast_db()
>>> run.analyze(0.99)