QIIME pipeline

QIIME specifications


Unique identifier OMICS_01521
Alternative names Quantitative Insights Into Microbial Ecology, Denoiser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • Denoiser



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  • person_outline Rob Knight <>

Publication for Quantitative Insights Into Microbial Ecology

QIIME citations

PMCID: 5896095

[…] 515f and 806r [28], the v4 region was sequenced at bgi on the hiseq2500 sequencing platform (illumina). raw data from bgi was processed using a previously reported custom implementation [29] of qiime [30] with minor modifications which are described in detail in schneijderberg et al. (in preparation). in short, reads were quality filtered and filtered for chimeras using chimeraslayer. using […]

PMCID: 5865410

[…] and the lowest 9,541 per sample. one sample was excluded from the downstream analysis because of extremely low read count. the high quality filtered sequences from mothur were then transferred into qiime v.1.9.1 (caporaso et al., 2010). chimeras were detected in qiime using the uchime v.4.2.40 (edgar et al., 2011) pipeline, and operational taxonomic units (otu) (blaxter et al., 2005) […]

PMCID: 5527301

[…] pandaseq version 2.8 (53) using the default parameters of a quality threshold of 0.9, a minimum sequence overlap of 1 bp, and a minimum read length of 32 bp. the assembled sequences were analyzed by qiime (quantitative insights into microbial ecology) version 1.9.0 (54). the sequences were then clustered de novo with uparse (55) at 97% and 99% sequence identity, which also removed chimeras […]

PMCID: 5498539

[…] pair 909f (seq) and 1492r (seq)28. primer x was synthesized with unique tags to allow for sample identification55. sequences were analysed using the quantitative insights into microbial ecology (qiime) as described by caporaso et al.56. following quality checking for the removal of chimeras and ambiguous bases a total of 22474 reads were attributed to the samples used in this study […]

PMCID: 5428441

[…] phylum at 77%-80% identity, and unclassified at <77% identity66. we compared the sequences and analyzed the changes in bacterial ecology using quantitative insights into microbial ecology (qiime; http://qiime.sourceforge.net), bayesian, pynast, and unifrac67–69. the shannon diversity index h = –σp i ln(p i) and shannon equitability index eh = h/ln(s), where p i is the proportion […]

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.