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''' (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. | ||
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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. | 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. | ||
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eb Miniconda3-4.5.12.eb | eb Miniconda3-4.5.12.eb | ||
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conda activate qiime2-2019.7 | conda activate qiime2-2019.7 | ||
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Remember to log out and back in after "conda init bash" step. | Remember to log out and back in after "conda init bash" step. | ||
To use after installation, run: | To use after installation, run: | ||
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module load miniconda3 | module load miniconda3 | ||
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===Without conda environment (preferred)=== | ===Without conda environment (preferred)=== | ||
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 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: | ||
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eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb | eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb | ||
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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 step takes a while, but will provide you with the qiime/2019.7 module, that you have to load before using: | ||
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module load qiime2/2019.7 | module load qiime2/2019.7 | ||
</pre> | </pre> | ||
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=External Sources = | =External Sources = | ||
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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> | ||
Revision as of 22:32, 27 January 2020
QIIME (canonically 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 the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, 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.
Note: QIIME 2 has succeeded QIIME 1 as of January 1, 2018. Version 1 is no longer supported.
Usage
This software can be installed in your home directory using conda. It is not possible to install this software using pip at this time.
Installation Instructions
In Compute Canada we provide two ways of installing QIIME2: With and without conda environment.
With 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:
Instructions for installing QIIME 2 provided by the 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 "conda init bash" step.
To use after installation, run:
module load miniconda3 conda activate qiime2-2019.7
Without conda environment (preferred)
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:
eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb
This step takes a while, but will provide you with the qiime/2019.7 module, that you have to load before using:
module load qiime2/2019.7
External Sources
QIIME homepage
easybuild documentation
Getting started with Conda