QIIME: Difference between revisions

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'''QIIME''' (canonically pronounced chime) stands for Quantitative Insights Into [https://en.wikipedia.org/wiki/Microbial_ecology Microbial Ecology], is an open-source [https://en.wikipedia.org/wiki/Bioinformatics bioinformatics] pipeline for performing [https://en.wikipedia.org/wiki/Microbiota microbiome] analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the [https://www.illumina.com/ Illumina] or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, [https://en.wikipedia.org/wiki/Operational_taxonomic_unit OTU] picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.
'''QIIME''' (pronounced ''chime'') stands for ''Quantitative Insights Into [https://en.wikipedia.org/wiki/Microbial_ecology Microbial Ecology], is an open-source [https://en.wikipedia.org/wiki/Bioinformatics bioinformatics] pipeline for performing [https://en.wikipedia.org/wiki/Microbiota microbiome] analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on [https://www.illumina.com/ Illumina] or other platforms to publication-quality graphics and statistics. This includes demultiplexing and quality filtering, [https://en.wikipedia.org/wiki/Operational_taxonomic_unit OTU] picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.


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'''Note''': QIIME 2 has succeeded QIIME 1 as of January 1, 2018. Version 1 is no longer supported.
'''Note''': QIIME 2 has succeeded QIIME 1 as of January 1, 2018. Version 1 is no longer supported.


=Usage= <!--T:3-->
==Installation == <!--T:4-->
This software can be installed in your home directory using conda.  It is not possible to install this software using pip at this time.
QIIME 2 can be installed in your home directory using conda.  It is not possible to install this software using pip at this time.


==Installation Instructions== <!--T:4-->
The installation procedure depends on whether or not you are in a [https://www.anaconda.com/ conda] environment.
In Compute Canada we provide two ways of installing QIIME2: With and without [https://www.anaconda.com/ conda] environment.


===With conda environment=== <!--T:5-->
===With a conda environment=== <!--T:5-->
Although we '''do not recommend''' using conda environments in an HPC environment, we provide the option to do so at your own peril:
Although we '''do not recommend''' using conda environments in an HPC environment, we provide the option to do so at your own peril:


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Instructions for installing QIIME 2 provided by the developers are found [https://docs.qiime2.org/ here]. These instructions, adapted for Compute Canada systems, are given below for version 2019.7.  If a new version of the .yml file is released (check the link), use the newer version by updating the instructions below.
General installation instructions by the QIIME 2 developers are found [https://docs.qiime2.org/ here]. These instructions, adapted for Compute Canada systems, are given below for version 2019.7.  If a new version of the <tt>.yml</tt> file is released (check the link), use the newer version by updating the instructions below.
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Remember to log out and back in after "conda init bash" step.
Remember to log out and back in after the "conda init bash" step.


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To use after installation, run:
To run QIIME 2, use
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===Without conda environment (preferred)=== <!--T:9-->
===Without a conda environment (preferred)=== <!--T:9-->
Since we know that conda environments can create more problems that it solve in HPC systems, we provide easybuild packages, that can be used with the eb command. To install QIIME2 version 2019.7, you have to do:
Since we know that conda environments can create more problems that they solve in HPC systems, we provide EasyBuild packages that can be used with the <tt>eb</tt> command. To install version 2019.7, you have to use
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This step takes a while, but will provide you with the qiime/2019.7 module, that you have to load before using:
This takes a while, but will provide you with the qiime/2019.7 module that you need to load before using QIIME 2.
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=External Sources = <!--T:11-->
=References = <!--T:11-->
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[http://qiime.org/ QIIME homepage]<br>
[http://qiime.org/ QIIME homepage]<br>
[https://easybuild.readthedocs.io/en/latest/ easybuild documentation]<br>
[https://easybuild.readthedocs.io/en/latest/ EasyBuild documentation]<br>
[https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html Getting started with Conda]<br>
[https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html Getting started with Conda]<br>
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[[Category:Bioinformatics]]
[[Category:Bioinformatics]]
[[Category:User Installed Software]]
[[Category:User Installed Software]]

Revision as of 21:27, 30 January 2020

Other languages:

QIIME (pronounced chime) stands for Quantitative Insights Into Microbial Ecology, is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on Illumina or other platforms to publication-quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.

Note: QIIME 2 has succeeded QIIME 1 as of January 1, 2018. Version 1 is no longer supported.

Installation

QIIME 2 can be installed in your home directory using conda. It is not possible to install this software using pip at this time.

The installation procedure depends on whether or not you are in a conda environment.

With a conda environment

Although we do not recommend using conda environments in an HPC environment, we provide the option to do so at your own peril:

General installation instructions by the QIIME 2 developers are found here. These instructions, adapted for Compute Canada systems, are given below for version 2019.7. If a new version of the .yml file is released (check the link), use the newer version by updating the instructions below. 

eb Miniconda3-4.5.12.eb
module load miniconda3
conda update conda
wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml
conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml
conda init bash
conda activate qiime2-2019.7

Remember to log out and back in after the "conda init bash" step.

To run QIIME 2, use 

module load miniconda3
conda activate qiime2-2019.7

Without a conda environment (preferred)

Since we know that conda environments can create more problems that they solve in HPC systems, we provide EasyBuild packages that can be used with the eb command. To install version 2019.7, you have to use 

eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb

This takes a while, but will provide you with the qiime/2019.7 module that you need to load before using QIIME 2. 

module load qiime2/2019.7

References

QIIME homepage
EasyBuild documentation
Getting started with Conda

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