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.
Installation
StrainGE requires Python >= 3.7 and depends on the following packages:
NumPy
SciPy
matplotlib
scikit-bio
pysam
h5py
intervaltree
These packages will be automatically installed when installing through pip.
Install through pip
pip install strainge
Make sure numpy is already installed before installing StrainGE.
Install from bioconda
Create a new conda environment and activate it
conda create -n strainge python=3.9 source activate strainge
Add bioconda and conda-forge channels
conda config --add channels bioconda conda config --add channels conda-forge
Install StrainGE
conda install strainge
Tip: also consider installing Mamba for much faster conda operations.
Install manually from github
Clone the repository
git clone https://github.com/broadinstitute/StrainGE
Install StrainGE
cd StrainGE python setup.py install
Usage
Citation
If you use StrainGE in your project, please consider citing our publication:
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.