Getting Started with QIIME 2
QIIME 2 is distributed as a combination of domain/omic-specific base distributions and any additional plugins you may wish to install. Not all plugins are compatible (or necessarily useful) with all distributions, so compatibility with a base distribution is always indicated. The following base distributions are available:
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.