QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
By Evan Bolyen, J. Rideout, Matthew R. Dillon, Nicholas A. Bokulich, C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, F. Asnicar and 99 more. 2018
1,189 citations recorded by the source corpus.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Subfields: Biophysics, Information Systems and Management, Molecular Biology
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In Molecular Biology
- Michael Jeffrey Gandal
- Brajesh Kumar Singh
- Rosa Krajmalnik-Brown
- Michael Wagner
- Susan C. Baker
- H. Smidt
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- Elhanan Borenstein
Citations in the corpus
- Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019, methodology): “…sequencing was performed using MiSeq Illumina platform (MiSeq Reagent Kit v2; Illumina Inc.; San Diego, CA, USA) and microbiome sequencing data were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME2) software package (Bolyen et al., 2018; Caporaso et al., 2010).”
- A practical guide to DNA metabarcoding for entomological ecologists (2020, methodology): “4/interfaces/q2studio/) (Bolyen et al., 2018) Functional prototype of a graphical user interface version for qiime2 Bioinformatics tools are adapted to plugins in q2studio.”
- Microbiome definition re-visited: old concepts and new challenges (2020, methodology): “For performing the data evaluations of 16S rRNA gene sequences, free software solutions and wellworking forums like Qiime2 [159] and Mothur [160] are available.”