Data

Tools

Indexes

Applications

Experiments

Open Source Science

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

Viral genomics analysis pipelines

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

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    8 of 19 committers (42.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary

Keywords

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

Keywords from Contributors

bioinformatics workflow-management carpentries
Last synced: 6 months ago · JSON representation

Repository

Viral genomics analysis pipelines

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 64.5 MB
Statistics
  • Stars: 192
  • Watchers: 29
  • Forks: 68
  • Open Issues: 64
  • Releases: 0
Topics
bam fastq genome genome-assembly genome-sequencing genomics illumina variant-annotations variant-calling viral viral-ngs
Created over 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

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/

Docker Repository on Quay Build Status Coverage Status Code Health Documentation Status DOI

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.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Watch event: 7
  • Fork event: 1
Last Year
  • Watch event: 7
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 2,372
  • Total Committers: 19
  • Avg Commits per committer: 124.842
  • Development Distribution Score (DDS): 0.503
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Danny Park d****k@b****g 1,179
Christopher Tomkins-Tinch t****c@b****g 594
Chris Tomkins-Tinch t****c@g****m 169
Irwin Jungreis i****r@c****u 159
Simon Ye m****l@y****m 90
Ilya Shlyakhter i****l@a****u 52
Simon Ye s****7@g****m 45
Hayden Metsky h****y@g****m 41
Hanna Mendes Levitin h****n@g****m 19
Mike Lin m****n@m****t 9
Aaron Lin 0****l@g****m 3
biocyberman b****n@g****m 3
Christopher Tomkins-Tinch t****c@z****g 2
Christopher Tomkins-Tinch t****c@p****g 2
Lydia Andreyevna Krasilnikova l****s@m****u 1
Christopher Tomkins-Tinch t****c@h****g 1
pvanheus p****h@w****a 1
Brett T. Hannigan b****n@d****m 1
Katrin Leinweber 9****r 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 2 dnanexus.com: 1 webbedfeet.co.za: 1 hw-uger-1000.broadinstitute.org: 1 mit.edu: 1 platinum.broadinstitute.org: 1 ztest2001.broadinstitute.org: 1 mlin.net: 1 alum.mit.edu: 1 yesimon.com: 1 csail.mit.edu: 1

Dependencies

requirements-conda-tests.txt pypi
  • attrs =19.1.0 test
  • coverage =4.5.2 test
  • coveralls =1.3.0 test
  • flake8 >=3.2.1 test
  • lxml =4.3.3 test
  • mock =2.0.0 test
  • pycodestyle =2.2.0 test
  • pytest =4.2.0 test
  • pytest-cov ==2.6.1 test
  • pytest-mock =1.10.0 test
  • pytest-xdist =1.26.1 test
  • six =1.10.0 test
requirements-conda.txt pypi
  • PyYAML =5.1
  • arrow =0.12.1
  • bbmap =38.56
  • bedtools =2.28.0
  • biopython =1.72
  • blast =2.7.1
  • bmtagger =3.101
  • bwa =0.7.17
  • cd-hit =4.6.8
  • cd-hit-auxtools =4.6.8
  • diamond =0.9.10
  • fastqc =0.11.7
  • future ==0.16.0
  • gap2seq =3.1.1a2
  • gatk =3.8
  • kaiju =1.6.3_yesimon
  • kmc =3.1.1rc1
  • krakenuniq =0.5.7_yesimon
  • krona =2.7.1
  • last =876
  • lbzip2 =2.5
  • lz4-c =1.9.1
  • mafft =7.402
  • matplotlib =2.2.4
  • mummer4 =4.0.0beta2
  • muscle =3.8.1551
  • mvicuna =1.0
  • novoalign =3.07.00
  • parallel =20160622
  • picard-slim =2.21.1
  • pigz =2.4
  • prinseq =0.20.4
  • pybedtools =0.7.10
  • pysam =0.15.0
  • r-base =3.5.1
  • samtools =1.9
  • snpeff =4.3.1t
  • spades =3.12.0
  • tbl2asn =25.6
  • trimmomatic =0.38
  • trinity =date.2011_11_26
  • unzip =6.0
  • vphaser2 =2.0
requirements-minimal.txt pypi
  • PyYAML =5.1
  • biopython =1.72
  • fastqc =0.11.7
  • future ==0.16.0
  • lbzip2 =2.5
  • lz4-c =1.9.1
  • matplotlib =2.2.4
  • picard-slim =2.21.1
  • pigz =2.4
  • pybedtools =0.7.10
  • pysam =0.15.0
  • samtools =1.9
  • unzip =6.0
requirements-py-docs.txt pypi
  • PyYAML ==5.1
  • Sphinx ==1.4.4
  • matplotlib ==2.2.4
  • mock >=2.0.0
  • sphinx-argparse ==0.1.15
  • sphinx_rtd_theme ==0.1.9
requirements-py3.txt pypi
  • boto3 *
  • filechunkio >=1.8
  • google-cloud-storage *
  • pysftp >=0.2.8
  • snakemake ==5.6.0