QIIME (English: /tʃaɪm/ 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[1][2] and QIIME 2.[3][4]

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 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 QIIME 2 Forum.[5]

"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).

See also

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References

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  1. ^ "QIIME". qiime.org. Retrieved 2024-01-19.
  2. ^ Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse; Bittinger, Kyle; et al. (May 2010). "QIIME allows analysis of high-throughput community sequencing data". Nature Methods. 7 (5): 335–336. doi:10.1038/nmeth.f.303. PMC 3156573.
  3. ^ "QIIME 2". qiime2.org. Retrieved 2024-01-19.
  4. ^ Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R.; Bokulich, Nicholas A.; et al. (August 2019). "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2". Nature Biotechnology. 37 (8): 852–857. doi:10.1038/s41587-019-0209-9. hdl:1721.1/125325. PMC 7015180.
  5. ^ "QIIME 2 has succeeded QIIME 1". QIIME News and Announcements. 2018-01-03. Retrieved 2024-01-19.

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16S ribosomal RNA

bioinformatics tools such as ANI calculator, ContEst16S and 16S rRNA DB for QIIME and Mothur pipeline. MIMt is a compact non-redundant 16S database for a

Chimera (molecular biology)

PMID 8594608. "Chimera checking sequences with QIIME". Quantitative Insights Into Microbial Ecology (QIIME). Retrieved 2019-01-10. Edgar R. "UCHIME algorithm"

Ancient DNA

been developed for pathogen and microorganism aDNA analyses in a small (QIIME) and large scale (FALCON ). Taking preventative measures in their procedure

Microbiota

the available information. Tools used to analyze the data include VAMPS, QIIME, mothur and DADA2 or UNOISE3 for denoising. Metagenomics is also used extensively

Metabarcoding

Widmann, Jeremy; Yatsunenko, Tanya; Zaneveld, Jesse; Knight, Rob (2010). "QIIME allows analysis of high-throughput community sequencing data". Nature Methods

DNA barcoding

The most frequently used bioinformatic software include Mothur, Uparse, Qiime, Galaxy, Obitools, JAMP, Barque, and DADA2. Comparing the abundance of reads

MG-RAST

clusters of proteins at 90% identity level using the UCLUST implementation in QIIME. The longest sequence of each cluster will be selected for a similarity

Rhizosphere

microbial community. Bioinformatics Analysis: Using software pipelines (e.g., QIIME, Mothur) to process sequencing data, calculate diversity indices, and compare