PT  - JOURNAL ARTICLE
AU  - Daniel B Goodman
AU  - Gleb Kuznetsov
AU  - Marc J. Lajoie
AU  - Brian W. Ahern
AU  - Michael G. Napolitano
AU  - Kevin Y. Chen
AU  - Changping Chen
AU  - George M. Church
TI  - Millstone: Software for Multiplex Microbial Genome Analysis and Engineering
AID  - 10.1101/086868
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 086868
4099  - http://biorxiv.org/content/early/2016/11/10/086868.short
4100  - http://biorxiv.org/content/early/2016/11/10/086868.full
AB  - Inexpensive 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 which 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.