Phage pipeline repo: v1.0

Contains pipeline going from protein data through mmseqs2 clustering and profile construction, all vs all HMM comparison to pairwise coverage comparison.

Required software:

• mmseqs2
• HHSuite (with databases)
• bgzip

Required Python libraries (as in requirements.txt file):

• biopython==1.78
• csb==1.2.5
• notebook==6.3.0
• scikit-learn==0.24.2
• seaborn==0.11.1

Environment

• Pipeline should be run in virtual environment created with virtualenv
• Pipeline was tested on Python3.9/MacOS and production run was made on Python3.6/Linux