title: Grinder: a versatile amplicon and shotgun sequence simulator.
abstract: 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.
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia. florent.angly@gmail.com
authors.forename: Florent E
authors.initials: FE
authors.lastname: Angly
authors.forename: Dana
authors.initials: D
authors.lastname: Willner
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Gene W
authors.initials: GW
authors.lastname: Tyson
mesh_terms: D003198:Computer Simulation; D015723:Gene Library; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S