Project-cluster

Identify and count clusters across a series of .sam files.

Usage

python run.py --help

Install

git clone https://github.com/DomBennett/Project-cluster.git

Or download the zipped folder:

wget https://github.com/DomBennett/Project-cluster/archive/master.zip

Requirements

• One .sam file stored per folder
• cdhit
• Python (v2 or v3)

Steps

• Convert .sam to .fasta by extracting the orthologous sequence identified within the .sam file.
• Run cdhit
• Count clusters with greater than min_nsqs
• Report number of clusters per .sam in a .csv

Authors

D.J. Bennett & J.S. Eriksson