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

Viral genomics analysis pipelines
https://github.com/broadinstitute/viral-ngs

bam fastq genome genome-assembly genome-sequencing genomics illumina variant-annotations variant-calling viral viral-ngs

Last synced: about 2 months ago
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Viral genomics analysis pipelines

• Host: GitHub
• URL: https://github.com/broadinstitute/viral-ngs
• Owner: broadinstitute
• License: other
• Created: 2014-09-25T19:00:24.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2020-11-03T15:21:50.000Z (over 4 years ago)
• Last Synced: 2024-07-13T00:30:28.762Z (10 months ago)
• Topics: bam, fastq, genome, genome-assembly, genome-sequencing, genomics, illumina, variant-annotations, variant-calling, viral, viral-ngs
• Language: Python
• Homepage:
• Size: 64.5 MB
• Stars: 186
• Watchers: 29
• Forks: 66
• Open Issues: 64
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-virome - Viral-NGS - Broad Institute's viral genomic analysis on cloud. [Python] (Other Tools / Cloud-based Viral Analysis)

README

        
DEPRECATION WARNING

---------

This repository ([`broadinstitute/viral-ngs`](https://github.com/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/

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[![Coverage Status](https://coveralls.io/repos/broadinstitute/viral-ngs/badge.png)](https://coveralls.io/r/broadinstitute/viral-ngs)

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[![Documentation Status](https://readthedocs.org/projects/viral-ngs/badge/?version=latest)](http://viral-ngs.readthedocs.io/en/latest/?badge=latest)

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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.