This code is associated with the paper from Bonham et al., "Extensive horizontal gene transfer in cheese-associated bacteria". eLife, 2017. http://dx.doi.org/10.7554/eLife.22144

#Kvasir

Dependencies:

• Python 2.7 or 3.6
• MongoDB
  • pymongo
• BioPython
• Pandas (for dealing with distance matrices)
• 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.

Kvasir is a Norse god associated with fermented beverages. According to Wikipedia,

Extremely wise, Kvasir traveled far and wide, teaching and spreading knowledge. This continued until the dwarfs Fjalar and Galar killed Kvasir and drained him of his blood. The two mixed his blood with honey, resulting in the Mead of Poetry, a mead which imbues the drinker with skaldship and wisdom, and the spread of which eventually resulted in the introduction of poetry to mankind.

Installation

The easiest way to use Kvasir is to install it from pypi:

$ pip install kvasirHGT

Take a look at the docs for usage information.