strainge 1.1.5

Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.

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.

Dependencies

Python packages

• Python >= 3.7
• NumPy
• SciPy
• matplotlib
• scikit-bio >= 0.5
• scikit-learn >= 0.24
• 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.

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.