Millstone: software for multiplex microbial genome analysis and engineering

Daniel B Goodman; Gleb Kuznetsov; Marc J Lajoie; Brian W Ahern; Michael G Napolitano; Kevin Y Chen; Changping Chen; George M Church

doi:10.1186/s13059-017-1223-1

Millstone: software for multiplex microbial genome analysis and engineering

Genome Biol. 2017 May 25;18(1):101. doi: 10.1186/s13059-017-1223-1.

Authors

Daniel B Goodman^{1

2}, Gleb Kuznetsov^{1

2

3}, Marc J Lajoie^{1

2}, Brian W Ahern⁴, Michael G Napolitano^{1

2

5}, Kevin Y Chen⁴, Changping Chen⁴, George M Church^{6

7}

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA, USA.
² Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.
³ Program in Biophysics, Harvard University, Boston, MA, USA.
⁴ Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
⁶ Department of Genetics, Harvard Medical School, Boston, MA, USA. gchurch@genetics.med.harvard.edu.
⁷ Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA. gchurch@genetics.med.harvard.edu.

Abstract

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 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.

Keywords: Bioinformatics; Experimental evolution; Genome engineering; Laboratory evolution; Microbial evolution; Synthetic biology; Synthetic genomics; Whole-genome sequencing.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology / instrumentation*
Genome
Genome, Microbial / genetics*
Genomics*
Genotype
High-Throughput Nucleotide Sequencing
Internet
Oligonucleotides / genetics
Software*

Substances

Oligonucleotides

Grants and funding

T32 GM008313/GM/NIGMS NIH HHS/United States