InStrain was developed by Matt Olm and Alex Crits-Christoph in the Banfield Lab at the University of California, Berkeley.

Special thanks to all those who have provided feedback on GitHub and otherwise, especially early adopters Keith Bouma-Gregson, Ben Siranosian, Yue “Clare” Lou, Naïma Madi, and Antônio Pedro Camargo.

Many of the ideas in Important concepts were honed over many years during countless discussions with members of the Banfield Lab, the Sonnenburg Lab, and others. Special thanks to Christopher Brown, Keith Bouma-Gregson, Yue “Clare” Lou, Spencer Diamond, Alex Thomas, Patrick West, Alex Jaffe, Bryan Merrill, Matt Carter, and Dylan Dahan.


InStrain relies on several previously published programs and python modules to run - see here and here for a full list of dependencies. Of special importance are samtools (the basis for parsing .bam files) and coverM (the heart of quick_profile).

While not a direct dependency, the open-source program anvi’o was used as significant inspiration for several implementation details, especially related to multiprocessing efficiency and memory management.


The manuscript describing inStrain is available in Nature Biotechnology and on bioRxiv and can be cited as follows:

Olm, M.R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B.A., Morowitz, M.J., Banfield, J.F., 2021. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nature Biotechnology.