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| [](https://quay.io/repository/broadinstitute/viral-core) | ||
| [](https://travis-ci.com/broadinstitute/viral-core) | ||
| [](https://coveralls.io/github/broadinstitute/viral-core?branch=master) | ||
| [](http://viral-core.readthedocs.io/en/latest/?badge=latest) | ||
| <!-- | ||
| [](https://coveralls.io/github/broadinstitute/viral-core?branch=master) | ||
| [](https://anaconda.org/broad-viral/viral-ngs) | ||
| [](http://viral-ngs.readthedocs.io/en/latest/?badge=latest) | ||
| [](https://landscape.io/github/broadinstitute/viral-ngs) | ||
| [](https://doi.org/10.5281/zenodo.252549) | ||
| --> | ||
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| viral-ngs | ||
| viral-core | ||
| ========= | ||
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| A set of scripts and tools for the analysis of viral NGS data. | ||
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| More detailed command line documentation can be found at [readthedocs](http://viral-core.readthedocs.org/) | ||
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| Developer documentation can be found at [here](DEVELOPMENT_NOTES.md) | ||
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| 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. | ||
| Higher level pipelines and workflows for viral-ngs can be found in the [pipelines github repo](https://github.com/broadinstitute/viral-pipelines). |