strainge

v1.3.9

Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains. For more information about how to use this package see README

Latest version published 1 year ago

License: BSD-3-Clause

PyPI

GitHub

Package Health Score

63 / 100

security
No known security issues
popularity
Recognized
maintenance
Inactive
community
Active

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Popularity

Recognized

GitHub Stars: 6.76K
Forks: 347
Contributors: 150

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package strainge, we found that it has been starred 6,759 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Nov 1, 2023
Direct Vulnerabilities: 0
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0
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Indirect Vulnerabilities: 0
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License Risk: 0
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

BSD-3-Clause

Security Policy

Yes

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Maintenance

Inactive

Commit Frequency

Open Issues: 516
Open PR: 45
Last Release: 1 year ago
Last Commit: 2 months ago

Further analysis of the maintenance status of strainge based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

An important project maintenance signal to consider for strainge is that it hasn't seen any new versions released to PyPI in the past 12 months, and could be considered as a discontinued project, or that which receives low attention from its maintainers.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: No
Contributors: 150
Funding: No

A good and healthy external contribution signal for strainge project, which invites more than one hundred open source maintainers to collaborate on the repository.

We found a way for you to contribute to the project! Looks like strainge is missing a Code of Conduct.

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Package

Python Versions Compatibility: >=3.8

Age: 4 years
Latest Release: 1 year ago
Dependencies: 8 Direct
Versions: 21
Maintainers: 1
Wheels: Linux, macOS, Musllinux

Readme

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.

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

Install Anaconda or miniconda (if not already present on your system)
Create a new environment:

conda create -n strainge python=3
Activate the environment:

source activate strainge

Enable bioconda and conda-forge channels:

conda config --add channels bioconda
conda config --add channels conda-forge

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.

strainge dependencies

h5py intervaltree matplotlib numpy pysam scikit-bio scikit-learn scipy

FAQs

What is strainge?

Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains. Visit Snyk Advisor to see a full health score report for strainge, including popularity, security, maintenance & community analysis.

Is strainge popular?

The python package strainge receives a total of 1,506 weekly downloads. As such, strainge popularity was classified as a recognized. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is strainge well maintained?

We found indications that strainge is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is strainge safe to use?

The python package strainge was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 23 November-2024, at 14:34 (UTC).

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