Grinder: a versatile amplicon and shotgun sequence simulator

Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012) Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 12: e94.1-e94.8. doi:10.1093/nar/gks251

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Author Angly, Florent E.
Willner, Dana
Rohwer, Forest
Hugenholtz, Philip
Tyson, Gene W.
Title Grinder: a versatile amplicon and shotgun sequence simulator
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2012-07
Sub-type Article (original research)
DOI 10.1093/nar/gks251
Open Access Status DOI
Volume 40
Issue 12
Start page e94.1
End page e94.8
Total pages 8
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2013
Language eng
Abstract We introduce Grinder ( 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.
Keyword 454 pyrosequencing data
Ribosomal-RNA gene
Microbial diversity
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

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