QIIME statistics

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Protocols

QIIME specifications

Information


Unique identifier OMICS_01521
Name QIIME
Alternative name Quantitative Insights Into Microbial Ecology
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Haskell, Javascript, Python, R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Subtool


  • Denoiser

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Rob Knight
  • person_outline J. Gregory Caporaso

Additional information


https://docs.qiime2.org/2018.6/ The previous version can be found at https://github.com/biocore/qiime

Publications for Quantitative Insights Into Microbial Ecology

QIIME citations

 (3520)
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Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial

2018
MBio
PMCID: 5964358
DOI: 10.1128/mBio.02392-17
call_split See protocol

[…] l can be found on the website http://drive5.com/usearch/manual/uparse_pipeline.html. The detailed procures were stated in our previous publication (). α- and β-diversity analyses were performed using QIIME v1.8.0 (). To normalize read depth, all samples were randomly subsampled to 5,000 reads/sample. Shannon’s index, Simpson’s index, rarefaction, and Chao1 estimates were evaluated. A normalized an […]

call_split

Food Starch Structure Impacts Gut Microbiome Composition

2018
PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18
call_split See protocol

[…] The raw 16S rRNA gene sequence data were analyzed by Quantitative Insight Into Microbial Ecology (QIIME) version 1.9.1 (). Sequences with a Phred score of lower than 20 were removed. Chimeric sequences were checked and removed using USEARCH version 6.1.544 (). The remaining high-quality reads were […]

library_books

American Gut: an Open Platform for Citizen Science Microbiome Research

2018
mSystems
PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] eference to identify reasonable placements for sequence fragments within an existing phylogeny and alignment. Taxonomy was assigned using an implementation of the RDP classifier () as implemented in QIIME2 (). Multiple rarefactions were computed, with the minimum being 1,250 sequences per sample with the analyses using the 1,250-sequence set except where noted explicitly. Rarefaction was used to […]

library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] ity within the cluster was 0.80. The largest clusters of trees were visualized with DensiTree 2.2.5 [] and a strict consensus tree was calculated for each cluster with the consensus_tree.py script in QIIME, using only nodes occurring more than 50% of the time [].Phylogenies of RNA polymerase II and beta tubulin genes were estimated by automatically aligning the nucleotide sequences with MAFFT [], […]

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Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

2018
mSystems
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17
call_split See protocol

[…] read pairs were merged using the USEARCH v7 program fastq_mergepairs, allowing stagger but no mismatches (). Operational taxonomic units (OTUs) were picked using the closedreference picking script in QIIME v1.7.0 and the Greengenes database (August 2013 release) (). The similarity threshold was set at 97%, reverse read matching was enabled, and reference-based chimera calling was disabled. The unf […]

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Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community

2018
Microbiome
PMCID: 5946436
PMID: 29751830
DOI: 10.1186/s40168-018-0475-7

[…] ”. For OTU identification, the 16S rRNA gene sequences were subjected to BLASTN search against the NCBI 16S ribosomal RNA database. Ecological analyses were performed using the vegan package in R and QIIME2 scripts. […]

Citations

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QIIME funding source(s)
Supported in part by a grant from the National Science Foundation.

QIIME review

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This is what you should use to study microbial ecology, diversity, communities , or any thing related to DNA metabarcoding.