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. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with...

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Autores principales: Goodman, Daniel B., Kuznetsov, Gleb, Lajoie, Marc J., Ahern, Brian W., Napolitano, Michael G., Chen, Kevin Y., Chen, Changping, Church, George M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445467/
https://www.ncbi.nlm.nih.gov/pubmed/28545559
http://dx.doi.org/10.1186/s13059-017-1223-1
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author Goodman, Daniel B.
Kuznetsov, Gleb
Lajoie, Marc J.
Ahern, Brian W.
Napolitano, Michael G.
Chen, Kevin Y.
Chen, Changping
Church, George M.
author_facet Goodman, Daniel B.
Kuznetsov, Gleb
Lajoie, Marc J.
Ahern, Brian W.
Napolitano, Michael G.
Chen, Kevin Y.
Chen, Changping
Church, George M.
author_sort Goodman, Daniel B.
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1223-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-54454672017-05-30 Millstone: software for multiplex microbial genome analysis and engineering Goodman, Daniel B. Kuznetsov, Gleb Lajoie, Marc J. Ahern, Brian W. Napolitano, Michael G. Chen, Kevin Y. Chen, Changping Church, George M. Genome Biol Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1223-1) contains supplementary material, which is available to authorized users. BioMed Central 2017-05-25 /pmc/articles/PMC5445467/ /pubmed/28545559 http://dx.doi.org/10.1186/s13059-017-1223-1 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
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
title Millstone: software for multiplex microbial genome analysis and engineering
title_full Millstone: software for multiplex microbial genome analysis and engineering
title_fullStr Millstone: software for multiplex microbial genome analysis and engineering
title_full_unstemmed Millstone: software for multiplex microbial genome analysis and engineering
title_short Millstone: software for multiplex microbial genome analysis and engineering
title_sort millstone: software for multiplex microbial genome analysis and engineering
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445467/
https://www.ncbi.nlm.nih.gov/pubmed/28545559
http://dx.doi.org/10.1186/s13059-017-1223-1
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