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Swabs to genomes: a comprehensive workflow

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library pre...

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Detalles Bibliográficos
Autores principales: Dunitz, Madison I., Lang, Jenna M., Jospin, Guillaume, Darling, Aaron E., Eisen, Jonathan A., Coil, David A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435499/
https://www.ncbi.nlm.nih.gov/pubmed/26020012
http://dx.doi.org/10.7717/peerj.960
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author Dunitz, Madison I.
Lang, Jenna M.
Jospin, Guillaume
Darling, Aaron E.
Eisen, Jonathan A.
Coil, David A.
author_facet Dunitz, Madison I.
Lang, Jenna M.
Jospin, Guillaume
Darling, Aaron E.
Eisen, Jonathan A.
Coil, David A.
author_sort Dunitz, Madison I.
collection PubMed
description The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
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spelling pubmed-44354992015-05-27 Swabs to genomes: a comprehensive workflow Dunitz, Madison I. Lang, Jenna M. Jospin, Guillaume Darling, Aaron E. Eisen, Jonathan A. Coil, David A. PeerJ Bioinformatics The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it. PeerJ Inc. 2015-05-14 /pmc/articles/PMC4435499/ /pubmed/26020012 http://dx.doi.org/10.7717/peerj.960 Text en © 2015 Dunitz et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Dunitz, Madison I.
Lang, Jenna M.
Jospin, Guillaume
Darling, Aaron E.
Eisen, Jonathan A.
Coil, David A.
Swabs to genomes: a comprehensive workflow
title Swabs to genomes: a comprehensive workflow
title_full Swabs to genomes: a comprehensive workflow
title_fullStr Swabs to genomes: a comprehensive workflow
title_full_unstemmed Swabs to genomes: a comprehensive workflow
title_short Swabs to genomes: a comprehensive workflow
title_sort swabs to genomes: a comprehensive workflow
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435499/
https://www.ncbi.nlm.nih.gov/pubmed/26020012
http://dx.doi.org/10.7717/peerj.960
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