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Grinder: a versatile amplicon and shotgun sequence simulator

We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA)...

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Detalles Bibliográficos
Autores principales: Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip, Tyson, Gene W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384353/
https://www.ncbi.nlm.nih.gov/pubmed/22434876
http://dx.doi.org/10.1093/nar/gks251
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author Angly, Florent E.
Willner, Dana
Rohwer, Forest
Hugenholtz, Philip
Tyson, Gene W.
author_facet Angly, Florent E.
Willner, Dana
Rohwer, Forest
Hugenholtz, Philip
Tyson, Gene W.
author_sort Angly, Florent E.
collection PubMed
description We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
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spelling pubmed-33843532012-06-28 Grinder: a versatile amplicon and shotgun sequence simulator Angly, Florent E. Willner, Dana Rohwer, Forest Hugenholtz, Philip Tyson, Gene W. Nucleic Acids Res Methods Online We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities. Oxford University Press 2012-07 2012-03-19 /pmc/articles/PMC3384353/ /pubmed/22434876 http://dx.doi.org/10.1093/nar/gks251 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Angly, Florent E.
Willner, Dana
Rohwer, Forest
Hugenholtz, Philip
Tyson, Gene W.
Grinder: a versatile amplicon and shotgun sequence simulator
title Grinder: a versatile amplicon and shotgun sequence simulator
title_full Grinder: a versatile amplicon and shotgun sequence simulator
title_fullStr Grinder: a versatile amplicon and shotgun sequence simulator
title_full_unstemmed Grinder: a versatile amplicon and shotgun sequence simulator
title_short Grinder: a versatile amplicon and shotgun sequence simulator
title_sort grinder: a versatile amplicon and shotgun sequence simulator
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384353/
https://www.ncbi.nlm.nih.gov/pubmed/22434876
http://dx.doi.org/10.1093/nar/gks251
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