Goodman, Daniel B.Kuznetsov, GlebLajoie, Marc J.Ahern, Brian W.Napolitano, Michael G.Chen, Kevin Y.Chen, ChangpingChurch, George2017-06-152017Goodman, Daniel B., Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen, and George M. Church. 2017. “Millstone: software for multiplex microbial genome analysis and engineering.” Genome Biology 18 (1): 101. doi:10.1186/s13059-017-1223-1. http://dx.doi.org/10.1186/s13059-017-1223-1.http://nrs.harvard.edu/urn-3:HUL.InstRepos:33029939Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1223-1) contains supplementary material, which is available to authorized users.en-USSynthetic biologyBioinformaticsSynthetic genomicsGenome engineeringMicrobial evolutionWhole-genome sequencingLaboratory evolutionExperimental evolutionJournal Article2017-06-1510.1186/s13059-017-1223-1