CGAT pipeline framework for programme viral track
Original methods by Bost et al.
https://www.sciencedirect.com/science/article/pii/S0092867420305687
https://github.com/PierreBSC/Viral-Track
Adapted by Lauren Overend (Lauren.overend@oriel.ox.ac.uk) and developed into a CGAT pipeline framework by Anna James-Bott
Set parameter values using pipeline_viral_track/pipeline.yml file. Run using pipeline_viral_track.py file
Requirements:
- STAR 2.6.1
- UMI-tools 1.0.0
- StringTie 2.1.0
- SAMtools 1.9
- R-bundle-Bioconductor/3.9
- Subread 1.6.4