StrainGE

A toolkit to track and characterize low-abundance strains using metagenomic data

StrainGE is a set of tools to analyse conspecific strain diversity in bacterial populations. It consists of two main components: 1) Strain Genome Search tool (StrainGST), a tool to find close reference genomes to strain(s) present in a sample and 2) Strain Genome Recovery (StrainGR), a tool to perform strain-aware variant calling at low coverages, which in turn can be used to track strains across samples.

_images/strainge-overview-full.png

Installation

StrainGE requires Python >= 3.7 and depends on the following packages:

  • NumPy

  • SciPy

  • matplotlib

  • scikit-bio

  • pyvcf

  • pysam

  • h5py

  • intervaltree

These packages will be automatically installed when installing through pip.

Install through pip

pip install strainge

Install manually from github

  1. Clone the repository

    git clone https://github.com/broadinstitute/StrainGE
    
  2. Install StrainGE

    cd StrainGE
    python setup.py install
    

Citation

If you use StrainGE in your project, please consider citing our publication: TODO

Indices and tables