Welcome to the QIIME 2 Library

This site is the hub for community distributed software, tutorials, and resources.
You can learn how to add your own plugins to this site here.

Recently Updated Plugins

q2-fmt

qiime2

q2-fmt is an all-in-one suite for assessing engraftment extent following Fecal Microbiota Transplants!

q2-annotate

bokulich-lab

QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.

q2-amrfinderplus

bokulich-lab

q2-amrfinderplus: QIIME 2 plugin to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences with AMRFinderPlus.

q2-kmerizer

bokulich-lab

QIIME 2 plugin for generating kmers from biological sequences

q2-picrust2

picrust

QIIME 2 plugin for PICRUSt2

q2-micom

micom-dev

A Qiime plugin for MICOM.

genome-sampler

caporaso-lab

genome-sampler: sample viral genomes across time of isolation, location of isolation, and genome divergence.

Discover more

Find new plugins and methods.

Base Distributions

Amplicon

A suite of plugins that provide broad analytic functionality to support microbiome marker gene analysis from raw sequencing data through publication quality visualizations and statistics.

MOSHPIT

MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking) is a toolkit of plugins for whole metagenome assembly, annotation, and analysis.

Pathogenome

A suite of plugins to detect viral genomes and protein sequences from MAGs and contigs for antimicrobial-resistance.

Tiny

A minimal installation of the QIIME 2 Framework for developers that is intended to be extended with custom functionality and plugins.

Books and Tutorials

Using QIIME 2

Your guide to becoming a QIIME 2 Framework power user.

Developing with QIIME 2

Your guide for writing, testing, and distributing QIIME 2 plugins, interfaces, and documentation.

q2-fmt book

genome-sampler documentation

Microbiome marker gene analysis with QIIME 2

Docs for MOSHPIT

QIIME 2 Cancer Microbiome Intervention Tutorial

This tutorial was originally developed for the 2022 NIH Foundation for Advanced Education in the Sciences Microbiome Bioinformatics with QIIME 2 workshop, taught online January 31 - February 4, 2022.

The tutorials

Moving Pictures tutorial 🎥

Gut-to-soil axis tutorial 💩🌱

Assessing engraftment extent with q2-FMT

Assessing Engraftment following an Auto-FMT using Amplicon Data. This tutorial was based on the publically available data from Taur et al. 2018.

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Find books and tutorials.

Latest Videos

Building a first QIIME 2 plugin

Building a first QIIME 2 plugin

Wed Apr 17 2024 QIIME 2

Expanding the impact of your microbiome study through metadata standardization

Expanding the impact of your microbiome study through metadata standardization

Tue Aug 09 2022 QIIME 2

Provenance replay demo (alpha software release)

Provenance replay demo (alpha software release)

Mon Jun 13 2022 QIIME 2

Longitudinal microbiome analysis

Longitudinal microbiome analysis

Tue May 17 2022 QIIME 2

Beta diversity visualizations

Beta diversity visualizations

Tue May 10 2022 QIIME 2

Alpha diversity visualizations

Alpha diversity visualizations

Tue May 03 2022 QIIME 2

Getting help with bioinformatics software

Getting help with bioinformatics software

Thu Apr 21 2022 QIIME 2

Watch more

Find recorded workshops and videos.