# Qiime2 2023.2
{{< admonition tip "Conda" true >}}
See the 'activating the conda environment' section below to access this
software.
{{< /admonition >}}
## qiime2-2023.2
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
researchers to start an analysis with raw DNA sequence data and finish with
publication-quality figures and statistical results.
Key features:
* Integrated and automatic tracking of data provenance
* Semantic type system
* Plugin system for extending microbiome analysis functionality
* Support for multiple types of user interfaces (e.g. API, command line, graphical)
QIIME 2 is a complete redesign and rewrite of the [QIIME
1](https://qiime.org/) microbiome analysis pipeline. QIIME 2 will address many
of the limitations of QIIME 1, while retaining the features that makes QIIME 1
a powerful and widely-used analysis pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
New functionality will regularly become available through QIIME 2 plugins. You
can view a list of plugins that are currently available on the QIIME 2
[plugin availability](https://docs.qiime2.org/2023.2/plugins/available/) page.
The [future plugins](https://docs.qiime2.org/2023.2/plugins/future/) page
lists plugins that are being developed.
-------------------------------------------------------------------------------
## Activating the conda environment
Check out a node with `qrsh` and run:
```console
bash
source /local/cluster/conda-envs/envs/qiime2/activate.sh
```
### Using conda activate qiime2
If your conda is set up as
[here](https://software.cqls.oregonstate.edu/tips/posts/using-the-system-miniconda-3-install/),
you can run `conda activate qiime2` instead of the `source` line above as well.
## Running over SGE
And then run your commands as usual. To use over SGE, include the source line
above in a shell script prior to your commands, e.g.
```bash
$ cat run_qiime2.sh
#!/usr/bin/env bash
source /local/cluster/conda-envs/envs/qiime2/activate.sh
qiime ...
```
And then run `hqsub 'bash ./run_qiime2.sh' -r sge.qiime2 ...`.
### Using hqsub --conda
You can also run:
`hqsub 'conda activate qiime2; qiime ...' -r sge.qiime2 --conda ...`
Without having to write a separate shell script.
## Location and version
```console
$ which qiime
/local/cluster/conda-envs/envs/qiime2-2023.2/bin/qiime
$ qiime version
Error: QIIME 2 has no plugin/command named 'version'.
$ qiime --version
q2cli version 2023.2.0
Run `qiime info` for more version details.
$ qiime info
System versions
Python version: 3.8.15
QIIME 2 release: 2023.2
QIIME 2 version: 2023.2.0
q2cli version: 2023.2.0
Installed plugins
alignment: 2023.2.0
composition: 2023.2.0
cutadapt: 2023.2.0
dada2: 2023.2.0
deblur: 2023.2.0
demux: 2023.2.0
diversity: 2023.2.0
diversity-lib: 2023.2.0
emperor: 2023.2.0
feast: 0.1.0
feature-classifier: 2023.2.0
feature-table: 2023.2.0
fragment-insertion: 2023.2.0
gneiss: 2023.2.0
longitudinal: 2023.2.0
metadata: 2023.2.0
phylogeny: 2023.2.0
quality-control: 2023.2.0
quality-filter: 2023.2.0
sample-classifier: 2023.2.0
sourcetracker2: 2.0.1-dev
taxa: 2023.2.0
types: 2023.2.0
vsearch: 2023.2.0
Application config directory
/local/cluster/conda-envs/envs/qiime2-2023.2/var/q2cli
Getting help
To get help with QIIME 2, visit https://qiime2.org
```
## help message
```console
$ qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...
QIIME 2 command-line interface (q2cli)
--------------------------------------
To get help with QIIME 2, visit https://qiime2.org.
To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:
source tab-qiime
To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:
autoload -Uz compinit && compinit
autoload bashcompinit && bashcompinit
source tab-qiime
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
diversity-lib Plugin for computing community diversity.
emperor Plugin for ordination plotting with Emperor.
feast Plugin for FEAST source-tracking
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
fragment-insertion Plugin for extending phylogenies.
gneiss Plugin for building compositional models.
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
sample-classifier Plugin for machine learning prediction of sample
metadata.
sourcetracker2 Plugin for source tracking.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
```
software ref:
research ref:
research ref: