QIIME

{{Short description|Microbiome multi-omics bioinformatics tool}}

QIIME ({{IPAc-en|lang|ʧ|aɪ|m}} {{respell|ch|eye|m}}) is a bioinformatics data science platform, originally developed for analysis of high-throughput microbiome marker gene (e.g., 16S or 18S rRNA genes) amplicon sequencing data. There have been two major versions of the QIIME platform, QIIME 1{{Cite web |title=QIIME |url=http://qiime.org/index-qiime1.html |access-date=2024-01-19 |website=qiime.org}} {{cite journal |display-authors=4 |last1=Caporaso |first1=J. Gregory |last2=Kuczynski |first2=Justin |last3=Stombaugh |first3=Jesse |last4=Bittinger |first4=Kyle |last5=Bushman |first5=Frederic D. |last6=Costello |first6=Elizabeth K. |last7=Fierer |first7=Noah |last8=Peña |first8=Antonio Gonzalez |last9=Goodrich |first9=Julia K. |last10=Gordon |first10=Jeffrey I. |last11=Huttley |first11=Gavin A. |last12=Kelley |first12=Scott T. |last13=Knights |first13=Dan |last14=Koenig |first14=Jeremy E. |last15=Ley |first15=Ruth E. |last16=Lozupone |first16=Catherine A. |last17=McDonald |first17=Daniel |last18=Muegge |first18=Brian D. |last19=Pirrung |first19=Meg |last20=Reeder |first20=Jens |last21=Sevinsky |first21=Joel R. |last22=Turnbaugh |first22=Peter J. |last23=Walters |first23=William A. |last24=Widmann |first24=Jeremy |last25=Yatsunenko |first25=Tanya |last26=Zaneveld |first26=Jesse |last27=Knight |first27=Rob |title=QIIME allows analysis of high-throughput community sequencing data |journal=Nature Methods |date=May 2010 |volume=7 |issue=5 |pages=335–336 |doi=10.1038/nmeth.f.303|pmc=3156573 }} and QIIME 2.{{Cite web |title=QIIME |url=http://qiime2.org |access-date=2024-01-19 |website=qiime2.org}} {{cite journal |display-authors=4 |last1=Bolyen |first1=Evan |last2=Rideout |first2=Jai Ram |last3=Dillon |first3=Matthew R. |last4=Bokulich |first4=Nicholas A. |last5=Abnet |first5=Christian C. |last6=Al-Ghalith |first6=Gabriel A. |last7=Alexander |first7=Harriet |last8=Alm |first8=Eric J. |last9=Arumugam |first9=Manimozhiyan |last10=Asnicar |first10=Francesco |last11=Bai |first11=Yang |last12=Bisanz |first12=Jordan E. |last13=Bittinger |first13=Kyle |last14=Brejnrod |first14=Asker |last15=Brislawn |first15=Colin J. |last16=Brown |first16=C. Titus |last17=Callahan |first17=Benjamin J. |last18=Caraballo-Rodríguez |first18=Andrés Mauricio |last19=Chase |first19=John |last20=Cope |first20=Emily K. |last21=Da Silva |first21=Ricardo |last22=Diener |first22=Christian |last23=Dorrestein |first23=Pieter C. |last24=Douglas |first24=Gavin M. |last25=Durall |first25=Daniel M. |last26=Duvallet |first26=Claire |last27=Edwardson |first27=Christian F. |last28=Ernst |first28=Madeleine |last29=Estaki |first29=Mehrbod |last30=Fouquier |first30=Jennifer |last31=Gauglitz |first31=Julia M. |last32=Gibbons |first32=Sean M. |last33=Gibson |first33=Deanna L. |last34=Gonzalez |first34=Antonio |last35=Gorlick |first35=Kestrel |last36=Guo |first36=Jiarong |last37=Hillmann |first37=Benjamin |last38=Holmes |first38=Susan |last39=Holste |first39=Hannes |last40=Huttenhower |first40=Curtis |last41=Huttley |first41=Gavin A. |last42=Janssen |first42=Stefan |last43=Jarmusch |first43=Alan K. |last44=Jiang |first44=Lingjing |last45=Kaehler |first45=Benjamin D. |last46=Kang |first46=Kyo Bin |last47=Keefe |first47=Christopher R. |last48=Keim |first48=Paul |last49=Kelley |first49=Scott T. |last50=Knights |first50=Dan |last51=Koester |first51=Irina |last52=Kosciolek |first52=Tomasz |last53=Kreps |first53=Jorden |last54=Langille |first54=Morgan G. I. |last55=Lee |first55=Joslynn |last56=Ley |first56=Ruth |last57=Liu |first57=Yong-Xin |last58=Loftfield |first58=Erikka |last59=Lozupone |first59=Catherine |last60=Maher |first60=Massoud |last61=Marotz |first61=Clarisse |last62=Martin |first62=Bryan D. |last63=McDonald |first63=Daniel |last64=McIver |first64=Lauren J. |last65=Melnik |first65=Alexey V. |last66=Metcalf |first66=Jessica L. |last67=Morgan |first67=Sydney C. |last68=Morton |first68=Jamie T. |last69=Naimey |first69=Ahmad Turan |last70=Navas-Molina |first70=Jose A. |last71=Nothias |first71=Louis Felix |last72=Orchanian |first72=Stephanie B. |last73=Pearson |first73=Talima |last74=Peoples |first74=Samuel L. |last75=Petras |first75=Daniel |last76=Preuss |first76=Mary Lai |last77=Pruesse |first77=Elmar |last78=Rasmussen |first78=Lasse Buur |last79=Rivers |first79=Adam |last80=Robeson |first80=Michael S. |last81=Rosenthal |first81=Patrick |last82=Segata |first82=Nicola |last83=Shaffer |first83=Michael |last84=Shiffer |first84=Arron |last85=Sinha |first85=Rashmi |last86=Song |first86=Se Jin |last87=Spear |first87=John R. |last88=Swafford |first88=Austin D. |last89=Thompson |first89=Luke R. |last90=Torres |first90=Pedro J. |last91=Trinh |first91=Pauline |last92=Tripathi |first92=Anupriya |last93=Turnbaugh |first93=Peter J. |last94=Ul-Hasan |first94=Sabah |last95=van der Hooft |first95=Justin J. J. |last96=Vargas |first96=Fernando |last97=Vázquez-Baeza |first97=Yoshiki |last98=Vogtmann |first98=Emily |last99=von Hippel |first99=Max |last100=Walters |first100=William |last101=Wan |first101=Yunhu |last102=Wang |first102=Mingxun |last103=Warren |first103=Jonathan |last104=Weber |first104=Kyle C. |last105=Williamson |first105=Charles H. D. |last106=Willis |first106=Amy D. |last107=Xu |first107=Zhenjiang Zech |last108=Zaneveld |first108=Jesse R. |last109=Zhang |first109=Yilong |last110=Zhu |first110=Qiyun |last111=Knight |first111=Rob |last112=Caporaso |first112=J. Gregory |title=Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 |journal=Nature Biotechnology |date=August 2019 |volume=37 |issue=8 |pages=852–857 |doi=10.1038/s41587-019-0209-9|hdl=1721.1/125325 |hdl-access=free }}

While microbiome marker gene analysis continues to be a major focus in QIIME 2, the developers describe it as a microbiome multi-omics platform, and support exists or is being added for analysis of shotgun metagenomics and metatranscriptomics data, as well as metabolomics mass spectrometry data.

Development of QIIME 1 was initiated in the Knight Lab at the University of Colorado at Boulder, and the first version of QIIME 1 was released on 26 January 2010. Beginning in August 2011, QIIME 1 development was led as a collaboration between the Caporaso Lab at Northern Arizona University and the Knight Lab.

In January 2018, QIIME 2 succeeded QIIME 1. QIIME 2 development is led by the [https://cap-lab.bio Caporaso Lab], but the project remains a community effort, with developers dispersed around the world. QIIME 2 users and developers can get help with the platform and network using the [https://forum.qiime2.org/ QIIME 2 Forum].{{Cite web |date=2018-01-03 |title=QIIME 2 has succeeded QIIME 1 |url=https://qiime.wordpress.com/2018/01/03/qiime-2-has-succeeded-qiime-1/ |access-date=2024-01-19 |website=QIIME News and Announcements |language=en}}

"QIIME" was originally coined as an acronym for Quantitative Insights Into Microbial Ecology, but since the development of QIIME 2 this acronym has not been used (e.g., the acronym was not referenced in the publication on QIIME 2).