inStrain is a python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

Manual, installation instructions, and expected output are at available at ReadTheDocs

Publication is available in Nature Biotechnology and on bioRxiv

$ pip install instrain

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

Docker image is available on Docker Hub at mattolm/instrain. See docker/ for use instructions.

$ inStrain -h

$ inStrain profile mapping.bam genome_file.fasta -o inStrain_profile1

$ inStrain compare inStrain_profile1 inStrain_profile2