Plugins¶
Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
The following pages describe what QIIME 2 plugins are available and how to develop a new plugin.
- Available plugins
- alignment: Plugin for generating and manipulating alignments.
- composition: Plugin for compositional data analysis.
- cutadapt: Plugin for removing adapter sequences, primers, and other unwanted sequence from sequence data.
- dada2: Plugin for sequence quality control with DADA2.
- deblur: Plugin for sequence quality control with Deblur.
- demux: Plugin for demultiplexing & viewing sequence quality.
- diversity: Plugin for exploring community diversity.
- diversity-lib: Plugin for computing community diversity.
- emperor: Plugin for ordination plotting with Emperor.
- feature-classifier: Plugin for taxonomic classification.
- feature-table: Plugin for working with sample by feature tables.
- fragment-insertion: Plugin for extending phylogenies.
- longitudinal: Plugin for paired sample and time series analyses.
- metadata: Plugin for working with Metadata.
- phylogeny: Plugin for generating and manipulating phylogenies.
- quality-control: Plugin for quality control of feature and sequence data.
- quality-filter: Plugin for PHRED-based filtering and trimming.
- rescript: Pipeline for reference sequence annotation and curation.
- sample-classifier: Plugin for machine learning prediction of sample metadata.
- stats: Plugin for statistical analyses.
- taxa: Plugin for working with feature taxonomy annotations.
- types: Plugin defining types for microbiome analysis.
- vizard: Generalized microbiome data visualization.
- vsearch: Plugin for clustering and dereplicating with vsearch.
- Future plugins
- Developing a QIIME 2 plugin