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.
StrainGE requires Python >= 3.7 and depends on the following packages:
These packages will be automatically installed when installing through pip.
Install through pip¶
pip install strainge
Install manually from github¶
Clone the repository
git clone https://github.com/broadinstitute/StrainGE
cd StrainGE python setup.py install
If you use StrainGE in your project, please consider citing our publication: TODO