viral-ngs

DEPRECATION WARNING

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

Pipelines are available here:

Pipeline documentation:

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.

Name		Name	Last commit message	Last commit date
Latest commit History 3,233 Commits
contrib		contrib
docker		docker
docs		docs
easy-deploy-script		easy-deploy-script
packaging/conda-recipe		packaging/conda-recipe
pipes		pipes
test		test
tools		tools
travis		travis
util		util
.agignore		.agignore
.coveragerc		.coveragerc
.dockerignore		.dockerignore
.flake8		.flake8
.gitattributes		.gitattributes
.gitignore		.gitignore
.landscape.yaml		.landscape.yaml
.pylintrc		.pylintrc
.style.yapf		.style.yapf
.travis.yml		.travis.yml
DEVELOPMENT_NOTES.md		DEVELOPMENT_NOTES.md
Dockerfile		Dockerfile
LICENSE		LICENSE
README.md		README.md
assembly.py		assembly.py
broad_utils.py		broad_utils.py
conftest.py		conftest.py
errors.py		errors.py
file_utils.py		file_utils.py
illumina.py		illumina.py
install_tools.py		install_tools.py
interhost.py		interhost.py
intrahost.py		intrahost.py
kmer_utils.py		kmer_utils.py
metagenomics.py		metagenomics.py
ncbi.py		ncbi.py
read_utils.py		read_utils.py
reports.py		reports.py
requirements-conda-tests.txt		requirements-conda-tests.txt
requirements-conda.txt		requirements-conda.txt
requirements-minimal.txt		requirements-minimal.txt
requirements-py-docs.txt		requirements-py-docs.txt
requirements-py3.txt		requirements-py3.txt
run_all_tests.sh		run_all_tests.sh
taxon_filter.py		taxon_filter.py