Qiime2 2023.2

2023-05-23 785 words 4 minutes

Contents

Conda

See the ‘activating the conda environment’ section below to access this software.

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 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 page. The future plugins page lists plugins that are being developed.

Activating the conda environment

Check out a node with qrsh and run:

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bash
source /local/cluster/conda-envs/envs/qiime2/activate.sh

Using conda activate qiime2

If your conda is set up as here, 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.

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$ 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

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$ 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

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$ 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: https://docs.qiime2.org/2023.2/
research ref: https://docs.qiime2.org/2023.2/citation/
research ref: https://doi.org/10.1038/s41587-019-0209-9