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:

  • 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
  2. Install StrainGE

    cd StrainGE
    python install


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

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