Acknowledgements

People

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.

Software

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.

Citation

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

Olm, M.R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B., Morowitz, M., Banfield, J., 2020. InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains. BioRxiv. https://doi.org/10.1101/2020.01.22.915579