QIIME
Description
QIIME (pronounced "chime") 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).
| QIIME version | Installed tools |
|---|---|
| qiime2 | available as part of 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.
Note: uclust command obsolete
The uclust command is obsolete and not longer supported on newer Linux (Debian 10 and higher) due to security reasons. It is not used in qiime2. If for some reason you need to use this command, we recommend to setup as Qiime virtual box http://qiime.org/install/virtual_box.html or on virtual machine in cloud with Debian 9.
License
Depends on used tool.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of qiime and load default version of qiime as
module avail qiime/ # list available modules module load qiime # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail qiime
and choose explicit version you want to use.
align_seqs.py -h
Qiime 1.x:
module add qiime-1.7.0 module add qiime-1.9.1
Qiime 2 as part of Conda - modules:
module add conda-modules conda env list export LANG=C.UTF-8 conda activate qiime2-2020.2
Documentation
http://qiime.org/documentation_index.html (Qiime 1.x - no longer supported!) https://qiime2.org/ (Qiime2)