Metadata-Version: 2.1
Name: strainge
Version: 1.0.3
Summary: Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.
Home-page: UNKNOWN
Author: Bruce Walker, Tim Straub, Lucas van Dijk
Author-email: bruce@broadinstitute.org, tstraub@broadinstitute.org, lvandijk@broadinstitute.org
License: UNKNOWN
Description: 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](https://readthedocs.org/projects/strainge/badge/?version=latest)](https://strainge.readthedocs.io/en/latest/?badge=latest)
        [![Python Package Index](https://img.shields.io/pypi/v/strainge)](https://pypi.org/project/strainge)
        [![DOI](https://zenodo.org/badge/71356920.svg)](https://zenodo.org/badge/latestdoi/71356920)
        
        
        
        Dependencies
        ------------
        
        ### Python packages
        
        * Python >= 3.7
        * NumPy
        * SciPy
        * matplotlib
        * scikit-bio >= 0.5
        * pyvcf
        * pysam
        * h5py
        * intervaltree
        
        ### Bioinformatics tools
        
        * bwa
        * samtools
        * mummer
        
        
        Installation
        ------------
        
        ### Python Package Index
        
        `pip install strainge`
        
        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. Clone the repository:
        
            `git clone https://github.com/broadinstitute/StrainGE`
        
        3. Move into the directory:
        
            `cd StrainGE`
        
        4. Create a new conda environment:
        
            `conda env create -f environment.yml`
        
        5. Activate the environment:
        
            `source activate strainge`
        
        
        Documentation
        -------------
        
        The documentation can be read on [readthedocs](https://strainge.readthedocs.io).
        
        Citation
        --------
        
        Dijk LR van, Walker BJ, Straub TJ, Worby C, Grote A, Schreiber HL, et al. StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities. bioRxiv. 2021 Feb 14;2021.02.14.431013. 
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
