DEPRECATION WARNING

This repository (broadinstitute/viral-ngs) is DEPRECATED; development now occurs in the following repositories:

https://github.com/broadinstitute/viral-core
https://github.com/broadinstitute/viral-assemble
https://github.com/broadinstitute/viral-phylo
https://github.com/broadinstitute/viral-classify

Pipelines are available here:

https://github.com/broadinstitute/viral-pipelines

Pipeline documentation:

https://viral-pipelines.readthedocs.io/en/latest/

viral-ngs

A set of scripts and tools for the analysis of viral NGS data.

More detailed documentation can be found at http://viral-ngs.readthedocs.org/
This includes installation instructions,
usage instructions for the command line tools,
and usage of the pipeline infrastructure.