skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

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. 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:
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 Org.:
AWS Cloud Credits for Research Program
OSTI Identifier:
1371690
Grant/Contract Number:  
FG02-02ER63445
Resource 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
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

Citation Formats

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., 2017. 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. Thu . "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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Millstone enables rapid iterative multiplex genome analysis and engineering. a To use Millstone, a researcher uploads a reference genome and next-generation sequencing reads for many individual genomic clones, for example from long-term evolution or targeted genome editing. Millstone performs alignment and variant calling for both single nucleotide variantsmore » and structural variation and then assigns predicted effects based on reference genome annotations. A unified data model stores sample genotype, phenotype, and variant annotation data. Variants can then be queried, filtered, and grouped into sets for export, triage, and analysis. These variant sets can be used to design oligonucleotides to recreate or revert mutations of interest, or used to generate new versions of the reference genome. b A combined screenshot of the Millstone analysis and alignment visualization views (condensed and cropped for clarity). A custom query language and a corresponding query form in the user interface allow searching and filtering over the data. As variant calls sometimes require visual inspection and comparison, Millstone’s variant analysis view provides programmatically generated links to visualizations of the relevant read alignments in JBrowse [18]« less

Save / Share:

Works referenced in this record:

Design, synthesis, and testing toward a 57-codon genome
journal, August 2016


Genomes by design
journal, August 2015

  • Haimovich, Adrian D.; Muir, Paul; Isaacs, Farren J.
  • Nature Reviews Genetics, Vol. 16, Issue 9
  • DOI: 10.1038/nrg3956

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
journal, May 2015


JBrowse: A next-generation genome browser
journal, July 2009

  • Skinner, M. E.; Uzilov, A. V.; Stein, L. D.
  • Genome Research, Vol. 19, Issue 9
  • DOI: 10.1101/gr.094607.109

Biocontainment of genetically modified organisms by synthetic protein design
journal, January 2015

  • Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.
  • Nature, Vol. 518, Issue 7537
  • DOI: 10.1038/nature14121

Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010


Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
journal, July 2011

  • Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H.
  • Science, Vol. 333, Issue 6040, p. 348-353
  • DOI: 10.1126/science.1205822

Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process
journal, April 2015

  • Shapland, Elaine B.; Holmes, Victor; Reeves, Christopher D.
  • ACS Synthetic Biology, Vol. 4, Issue 7
  • DOI: 10.1021/sb500362n

The Molecular Diversity of Adaptive Convergence
journal, January 2012

  • Tenaillon, O.; Rodriguez-Verdugo, A.; Gaut, R. L.
  • Science, Vol. 335, Issue 6067, p. 457-461
  • DOI: 10.1126/science.1212986

Genomically Recoded Organisms Expand Biological Functions
journal, October 2013

  • Lajoie, M. J.; Rovner, A. J.; Goodman, D. B.
  • Science, Vol. 342, Issue 6156, p. 357-360
  • DOI: 10.1126/science.1241459

RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013

  • Jiang, Wenyan; Bikard, David; Cox, David
  • Nature Biotechnology, Vol. 31, Issue 3, p. 233-239
  • DOI: 10.1038/nbt.2508

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

  • Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A.
  • Nature, Vol. 460, Issue 7257, p. 894-898
  • DOI: 10.1038/nature08187

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Adaptive laboratory evolution – principles and applications for biotechnology
journal, January 2013


    Works referencing / citing this record:

    Millstone: software for multiplex microbial genome analysis and engineering [Supplemental Data]
    figure, May 2017

    • Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.
    • figshare-Supplementary information for journal article at DOI: 10.1186/s13059-017-1223-1, 1 PDF file (2.17 MB)
    • DOI: 10.6084/m9.figshare.c.3788494

    Additional file 1 of Millstone: software for multiplex microbial genome analysis and engineering
    dataset, May 2017


      Figures / Tables found in this record:

        Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.