QIIME ( ) is a

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

data science platform, originally developed for analysis of high-throughput

microbiome A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps ''et al.'' as "a characteristic microbial community occupying a reasonably wel ...

marker gene In biology, a marker gene may have several meanings. In nuclear biology and molecular biology, a marker gene is a gene used to determine if a nucleic acid sequence has been successfully inserted into an organism's DNA. In particular, there are tw ...

(e.g., 16S or 18S rRNA genes)

amplicon In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication events. It can be formed artificially, using various methods including polymerase chain reactions (PCR) or ligase chain ...

sequencing data. There have been two major versions of the QIIME platform, QIIME 1 and QIIME 2. 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 Metagenomics is the study of all genetics, genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the mic ...

and

metatranscriptomics Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome. While metagenomics focuses on studying the genomic content and on identifying which microbes are prese ...

data, as well as

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerpri ...

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...

data. Development of QIIME 1 was initiated in the

Knight A knight is a person granted an honorary title of a knighthood by a head of state (including the pope) or representative for service to the monarch, the church, or the country, especially in a military capacity. The concept of a knighthood ...

Lab at the

University of Colorado at Boulder The University of Colorado Boulder (CU Boulder, CU, or Colorado) is a Public university, public research university in Boulder, Colorado, United States. Founded in 1876, five months before Colorado became a Federated state, state, it is the fla ...

, 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 Northern Arizona University (NAU) is a public research university based in Flagstaff, Arizona, United States. Founded in 1899, it was the third and final university established in the Arizona Territory. It is one of the three universities gove ...

and the Knight Lab. In January 2018, QIIME 2 succeeded QIIME 1. QIIME 2 development is led by th
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 th
QIIME 2 Forum
"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).

References

{{reflist, 2 Bioinformatics software Metagenomics

See also

References