Installation
The pages linked below provide conda and docker-based installation instructions for our base distributions, as well as the list of plugins built into each distribution, and links to relevant documentation. Other plugins can be installed in the resulting environments by following the instructions on the plugin pages. Plugin pages will provide information on which distribution(s) they are compatible with.
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.