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Open Source Science

https://github.com/broadinstitute/strainge

strain-level analysis tools

https://github.com/broadinstitute/strainge

Science Score: 57.0%

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

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
    Organization broadinstitute has institutional domain (www.broadinstitute.org)
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

strain-level analysis tools

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Size: 1.26 MB
Statistics
  • Stars: 39
  • Watchers: 12
  • Forks: 11
  • Open Issues: 16
  • Releases: 23
Created over 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

StrainGE: Strain-level Genome Exploration

StrainGE is a set of tools to analyse the within-species strain diversity in bacterial populations. It consists of two main components: 1) StrainGST: Strain Genome Search tool, a tool to find close reference genomes for strains present in a sample and 2) StrainGR: Strain Genome Recovery, a tool to perform strain-aware variant calling at low coverages.

Documentation Status Python Package Index DOI

Dependencies

Python packages

  • Python >= 3.7
  • NumPy
  • SciPy
  • matplotlib
  • scikit-bio >= 0.5
  • scikit-learn >= 0.24
  • pysam
  • h5py
  • intervaltree

Bioinformatics tools

  • bwa
  • samtools
  • mummer

Installation

Python Package Index

pip install strainge

Warning: NumPy already has to be installed otherwise the above command will fail. You'll have to make sure all tools like bwa, samtools and mummer are installed as well.

Conda

  1. Install Anaconda or miniconda (if not already present on your system)

  2. Create a new environment:

    conda create -n strainge python=3

  3. Activate the environment:

    source activate strainge

  4. Enable bioconda and conda-forge channels:

conda config --add channels bioconda conda config --add channels conda-forge 5. Install StrainGE:

conda install strainge

Optional tip: also consider installing mamba before installing StrainGE for much faster conda operations.

Documentation

The documentation can be read on readthedocs.

Citation

Dijk, Lucas R. van, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, et al. 2022. “StrainGE: A Toolkit to Track and Characterize Low-Abundance Strains in Complex Microbial Communities.” Genome Biology 23 (1): 74. https://doi.org/10.1186/s13059-022-02630-0.

Owner

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

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 2
  • Watch event: 5
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 1
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 5
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 1
  • Pull request event: 1
  • Fork event: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 49
  • Total pull requests: 5
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 22
  • Total pull request authors: 4
  • Average comments per issue: 1.63
  • Average comments per pull request: 0.2
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 7
  • Pull requests: 2
  • Average time to close issues: 2 days
  • Average time to close pull requests: about 2 months
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 1.29
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • nick-youngblut (7)
  • SilasK (4)
  • Ahmedbargheet (3)
  • drelo (2)
  • w1bw (1)
  • samnooij (1)
  • biolene (1)
  • qkqk-hub (1)
  • tstraub89 (1)
  • gavinmdouglas (1)
  • topfm (1)
  • sahilrishav2 (1)
  • sjmiller-sahmri (1)
  • joelewis101 (1)
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Pull Request Authors
  • dependabot[bot] (2)
  • nick-youngblut (1)
  • SilasK (1)
  • w1bw (1)
Top Labels
Issue Labels
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dependencies (2)

Dependencies

docs/requirements.txt pypi
  • IPython *
  • nbsphinx *
  • recommonmark *
  • sphinx *
requirements.txt pypi
  • h5py *
  • intervaltree *
  • matplotlib *
  • numpy *
  • pybind11 *
  • pysam *
  • scikit-bio *
  • scikit-learn *
  • scipy *
setup.py pypi
  • h5py *
  • intervaltree *
  • matplotlib *
  • numpy *
  • pysam *
  • scikit-bio >=0.5
  • scikit-learn >=0.24
  • scipy <1.9
.github/workflows/publish-pypa.yml actions
  • actions/checkout v3 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • pypa/cibuildwheel v2.11.4 composite
  • pypa/gh-action-pypi-publish master composite
environment.yml conda
  • bwa
  • h5py
  • matplotlib
  • mummer4
  • numpy
  • pip
  • pybind11
  • pysam >=0.19
  • python >=3.8
  • samtools >=1.15
  • scikit-bio >=0.5.8
  • scikit-learn >=0.24
  • scipy