This Github repository is to support the real-time genomic surveillance of the W. African Ebola epidemic 2014-2015 and the accompanying publication:
Real-time, portable genome sequencing for Ebola surveillance
Quick J, Loman N, et al.
Nature (2016) doi:10.1038/nature16996
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16996.html
The GitHub repository contains data, scripts and IPython notebooks to assist reproducibility and for others to build on this work for nanopore variant calling analysis.
At the moment some of the notebooks are a bit rough around the edges, but contain the key commands used.
Over the coming weeks I intend to continue adding detail to make the notebooks as user-friendly as possible for those unfamiliar with command-line bioinformatics, including details of installing all dependencies on a stock Ubuntu server.
I welcome pull requests and comments to n.j.loman@bham.ac.uk.