QIIME

module avail qiime/ # older version of qiime

module avail mambaforge/ # as an environment

QIIME and QIIME2 stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).

Usage

QIIME version	Installed tools
qiime2	available as part of mambaforge and conda-modules
qiime-1.9.1	biom-format, burrito, burrito-fillings, click, cogent, cycler, decorator, emperor, enum34, future, gdata, ipython, ipython-genutils, matplotlib, natsort, numpy, pandas, pathlib2, pexpect, pickleshare, Pygments, pynast, pyqi, scikit-bio, scipy
qiime-1.7.0	biom-format, blast, Cdbfasta, clearcut, fasttree, matplotlib, PyNAST, pyqi, raxml, RDP, rtax, tax2tree, uclust, usearch

Greengenes files are in /software/qiime/database/gg_13_8_otus.

QIIME2 in Mamba/Conda

Qiime 2 is installed as part of mambaforge and conda-modules:

module add mambaforge
mamba env list
export LANG=C.UTF-8
mamba activate qiime2-2020.2