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...

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Published inGenome biology Vol. 18; no. 1
Main Authors Goodman, Daniel B., Kuznetsov, Gleb, Lajoie, Marc J., Ahern, Brian W., Napolitano, Michael G., Chen, Kevin Y., Chen, Changping, Church, George M.
Format Journal Article
LanguageEnglish
Published United Kingdom Springer Science + Business Media 25.05.2017
Subjects
60 APPLIED LIFE SCIENCES
BASIC BIOLOGICAL SCIENCES
Bioinformatics
Experimental evolution
Genome engineering
Laboratory evolution
Microbial evolution
Synthetic biology
Synthetic genomics
Whole-genome sequencing
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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.
AbstractList 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.
Author Chen, Kevin Y.
Kuznetsov, Gleb
Ahern, Brian W.
Lajoie, Marc J.
Church, George M.
Chen, Changping
Napolitano, Michael G.
Goodman, Daniel B.
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  fullname: Church, George M.
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SubjectTerms 60 APPLIED LIFE SCIENCES
BASIC BIOLOGICAL SCIENCES
Bioinformatics
Experimental evolution
Genome engineering
Laboratory evolution
Microbial evolution
Synthetic biology
Synthetic genomics
Whole-genome sequencing
Title Millstone: software for multiplex microbial genome analysis and engineering
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