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Title: Millstone: software for multiplex microbial genome analysis and engineering

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. Here, 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.
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [4] ;  [3] ;  [3] ;  [1]
  1. Harvard Univ., Boston, MA (United States). Harvard Medical School, Dept. of Genetics; Harvard Univ., Boston, MA (United States). Harvard Medical School, Wyss Inst. for Biologically Inspired Engineering
  2. Harvard Univ., Boston, MA (United States). Harvard Medical School, Dept. of Genetics; Harvard Univ., Boston, MA (United States). Harvard Medical School, Wyss Inst. for Biologically Inspired Engineering; Harvard Univ., Boston, MA (United States). Program in Biophysics
  3. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  4. Harvard Univ., Boston, MA (United States). Harvard Medical School, Dept. of Genetics; Harvard Univ., Boston, MA (United States). Harvard Medical School, Wyss Inst. for Biologically Inspired Engineering; Harvard Univ., Boston, MA (United States). Harvard Medical School, Dept. of Biological and Biomedical Sciences
Publication Date:
Grant/Contract Number:
FG02-02ER63445
Type:
Accepted Manuscript
Journal Name:
Genome Biology (Online)
Additional Journal Information:
Journal Name: Genome Biology (Online); Journal Volume: 18; Journal Issue: 1; Related Information: Millstone genome engineering and analysis software: http://churchlab.github.io/millstone/; Journal ID: ISSN 1474-760X
Publisher:
BioMed Central
Research Org:
Harvard Univ., Boston, MA (United States). Harvard Medical School
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Contributing Orgs:
AWS Cloud Credits for Research Program
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Synthetic biology; Bioinformatics; Synthetic genomics; Genome engineering; Microbial evolution; Whole-genome sequencing; Laboratory evolution; Experimental evolution
OSTI Identifier:
1371690

Goodman, Daniel B., Kuznetsov, Gleb, Lajoie, Marc J., Ahern, Brian W., Napolitano, Michael G., Chen, Kevin Y., Chen, Changping, and Church, George M.. Millstone: software for multiplex microbial genome analysis and engineering. United States: N. p., Web. doi:10.1186/s13059-017-1223-1.
Goodman, Daniel B., Kuznetsov, Gleb, Lajoie, Marc J., Ahern, Brian W., Napolitano, Michael G., Chen, Kevin Y., Chen, Changping, & Church, George M.. Millstone: software for multiplex microbial genome analysis and engineering. United States. doi:10.1186/s13059-017-1223-1.
Goodman, Daniel B., Kuznetsov, Gleb, Lajoie, Marc J., Ahern, Brian W., Napolitano, Michael G., Chen, Kevin Y., Chen, Changping, and Church, George M.. 2017. "Millstone: software for multiplex microbial genome analysis and engineering". United States. doi:10.1186/s13059-017-1223-1. https://www.osti.gov/servlets/purl/1371690.
@article{osti_1371690,
title = {Millstone: software for multiplex microbial genome analysis and engineering},
author = {Goodman, Daniel B. and Kuznetsov, Gleb and Lajoie, Marc J. and Ahern, Brian W. and Napolitano, Michael G. and Chen, Kevin Y. and Chen, Changping and Church, George M.},
abstractNote = {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. Here, 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.},
doi = {10.1186/s13059-017-1223-1},
journal = {Genome Biology (Online)},
number = 1,
volume = 18,
place = {United States},
year = {2017},
month = {5}
}

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