Grinder: a versatile amplicon and shotgun sequence simulator

Nucleic Acids Research
Florent E AnglyGene W Tyson

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.

References

Sep 1, 1994·Computer Applications in the Biosciences : CABIOS·M L Engle, C Burks
Oct 9, 2002·Genome Research·Jason E StajichEwan Birney
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Sep 24, 2005·Saline Systems·Jinjun KanFeng Chen
Jul 6, 2006·Applied and Environmental Microbiology·Todd Z DeSantisG L Andersen
Aug 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Mitchell L SoginGerhard J Herndl
Nov 9, 2006·PLoS Biology·Florent E AnglyForest Rohwer
May 1, 2007·Nature Methods·Konstantinos MavromatisNikos C Kyrpides
Jul 31, 2007·Genome Biology·Susan M HuseDavid Mark Welch
Sep 27, 2008·Current Opinion in Microbiology·Susannah G Tringe, Philip Hugenholtz
Oct 9, 2008·PloS One·Daniel C RichterDaniel H Huson
May 7, 2009·Nucleic Acids Research·Yijun SunWilliam Farmerie
Jul 10, 2009·The ISME Journal·Vicente Gomez-AlvarezThomas M Schmidt
Aug 12, 2009·Nature Methods·Christopher QuinceWilliam T Sloan
Nov 17, 2009·Biometrics·Héctor Corrada Bravo, Rafael A Irizarry
Jan 15, 2010·PLoS Pathogens·Mahmoud A GhannoumPatrick M Gillevet
Mar 26, 2010·The ISME Journal·Bánk BeszteriStephen J Giovannoni
Apr 7, 2010·Proceedings of the National Academy of Sciences of the United States of America·Peter J TurnbaughJeffrey I Gordon
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
May 6, 2010·BMC Bioinformatics·Younghoon KimDoheon Lee
Apr 23, 2010·BMC Microbiology·Antoni BennasarElena García-Valdés
Jun 4, 2010·Genome Research·Ana P VivancosHeinz Himmelbauer
Nov 26, 2010·Nature Methods·Can AlkanEvan E Eichler
Nov 26, 2010·PLoS Biology·Howard OchmanPhilip Hugenholtz
Dec 1, 2010·Nature Methods·Suzan YilmazPhilip Hugenholtz
Jan 19, 2011·BMC Bioinformatics·Enis AfganJames Taylor
Feb 1, 2011·BMC Bioinformatics·Christopher QuincePeter J Turnbaugh
Mar 15, 2011·Current Protocols in Bioinformatics·Todd J TreangenMihai Pop
Jun 4, 2011·Bioinformatics·Simon A Berger, Alexandros Stamatakis
Jun 21, 2011·Bioinformatics·Susanne BalzerInge Jonassen
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Jul 22, 2011·Nature·Jonathan M RothbergJames Bustillo
Oct 8, 2011·American Journal of Respiratory Cell and Molecular Biology·Dana WillnerForest Rohwer

Citations

Oct 11, 2012·Bioinformatics·Robert A EdwardsRoss Overbeek
Oct 18, 2012·Bioinformatics·Bas E DutilhJohn L Mokili
Nov 7, 2012·Bioinformatics·Yukiteru OnoMichiaki Hamada
Sep 4, 2012·Nucleic Acids Research·Martin S Lindner, Bernhard Y Renard
Mar 21, 2013·Nucleic Acids Research·Connor T SkennertonGene W Tyson
Aug 31, 2013·PloS One·Matthew J MorganChristopher M Hardy
Oct 15, 2013·PloS One·Ben JiaChaochun Wei
Jan 15, 2014·PloS One·Mariel M FinucaneKatherine S Pollard
Apr 15, 2014·Bioinformatics·Josep GregoriJosep Quer
Feb 14, 2014·Nucleic Acids Research·Qichao TuJizhong Zhou
May 9, 2014·Bioinformatics·Saikat ChatterjeeJukka Corander
Jun 17, 2014·Bioinformatics·Serghei MangulEleazar Eskin
Sep 26, 2014·BMC Bioinformatics·Stephen JohnsonAnthony Kusalik
Nov 20, 2014·BMC Genomics·Daniel Aguirre de CárcerAntonio Alcamí
Mar 15, 2014·PloS One·David KoslickiGail Rosen
Aug 21, 2014·Environmental Microbiology Reports·Nicholas D Youngblut, Daniel H Buckley
Feb 3, 2016·Bioinformatics·Magali JaillardJean-Baptiste Veyrieras
May 20, 2015·Scientific Reports·Davide AlbaneseClaudio Donati
Apr 1, 2014·Scientific Reports·Cedric C LacznyPaul Wilmes
Sep 18, 2012·The New Phytologist·Sarah L LebeisPaul Schulze-Lefert
Nov 22, 2015·Bioinformatics·Kévin VervierJean-Philippe Vert
Nov 19, 2015·Scientific Reports·Ross Ka-Kit Leung, Ying-Kit Wu
Dec 15, 2015·Biotechnology Research International·Satish KumarManoj Pandit Brahmane
Jul 11, 2015·PeerJ·Katelyn McNair, Robert A Edwards
May 6, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Stefano R Bonissone, Pavel A Pevzner
Nov 14, 2015·PLoS Computational Biology·Stephen NayfachThomas J Sharpton
Aug 31, 2016·Nature Microbiology·Claudio DonatiNicola Segata
Jun 21, 2016·Nature Reviews. Genetics·Merly EscalonaDavid Posada
Aug 31, 2016·Proceedings of the National Academy of Sciences of the United States of America·Pilar ManriqueMark J Young
Jan 21, 2017·Microbiome·Jeremy W CoxAleksey Porollo
Apr 6, 2018·PloS One·Roberto SemeraroAlberto Magi
Nov 18, 2017·GigaScience·Matthew Z DeMaere, Aaron E Darling
Jul 12, 2017·Molecular Ecology Resources·Lucas AuerGuillermina Hernandez-Raquet
Jan 4, 2018·BMC Bioinformatics·Quang TranVinhthuy Phan
Jul 18, 2018·Bioinformatics·Hadrien GourléErik Bongcam-Rudloff
May 11, 2016·IEEE Transactions on Bio-medical Engineering·Xiguo YuanLiying Yang
Nov 9, 2016·MSystems·Nicholas A BokulichJ Gregory Caporaso
Jan 17, 2019·Bioinformatics·Subrata SahaSanguthevar Rajasekaran
Feb 21, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Romain Menegaux, Jean-Philippe Vert
Aug 27, 2017·Scientific Reports·Yuan JiangGuoxian Yu
Jun 22, 2019·Annual Review of Marine Science·Ferdi L Hellweger
Dec 24, 2019·Briefings in Functional Genomics·Shatha AlosaimiEmile R Chimusa
Nov 24, 2019·BMC Bioinformatics·Ilaria PatuzziBarbara Di Camillo
May 20, 2020·Briefings in Bioinformatics·Cécile HilpertDidier Debroas
Jun 10, 2020·Bioinformatics·David J Burks, Rajeev K Azad
Oct 6, 2020·Frontiers in Microbiology·Christine AnyansiThomas Abeel
Aug 2, 2018·BMC Bioinformatics·Antonino FiannacaAlfonso Urso
Dec 31, 2017·Letters in Applied Microbiology·C McCall, I Xagoraraki
Feb 10, 2019·Microbiome·Adrian FritzAlice C McHardy
Mar 30, 2020·The ISME Journal·Ruonan WuJames M Tiedje
Aug 15, 2018·Scientific Reports·Alejandra Escobar-ZepedaAlejandro Sanchez-Flores
Apr 5, 2020·BMC Bioinformatics·Sergey ShityakovThomas Dandekar
Nov 17, 2020·PeerJ·William C NelsonJennifer M Mobberley
Feb 7, 2021·Proceedings of the National Academy of Sciences of the United States of America·Sacha N CoeselE Virginia Armbrust
Feb 21, 2021·Interdisciplinary Sciences, Computational Life Sciences·Ningyuan FangDali Tong

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