InStrain is written in python. There are a number of ways that it can be installed.


To install inStrain using the PyPi python repository, simply run

$ pip install instrain

That’s it!

Pip is a great package with many options to change the installation parameters in various ways. For details, see pip documentation


To inStrain inStrain from bioconda, run

$ conda install -c conda-forge -c bioconda -c defaults instrain

From source

To install inStrain from the source code, run

$ git clone

$ cd instrain

$ pip install .


inStrain requires a few other programs to run. Not all dependencies are needed for all operations. There are a number of python package dependencies, but those should install automatically when inStrain is installed using pip



  • coverM This is needed for the quick_profile operation
  • Prodigal This is needed to profile on a gene by gene level

Pre-built genome database

An established set of public genomes can be downloaded for your inStrain analysis at the following link - See Tutorial #2 in Tutorial for usage instructions.

Docker image

A Docker image with inStrain and dependencies already installed is available on Docker Hub at mattolm/instrain. This image also has a wrapper script in it to make it easier to use inStrain with AWS. See the docker folder of the GitHub page for use instructions.