38,760
edits
QIIME/en: Difference between revisions
Jump to navigation
Jump to search
Updating to match new version of source page
(Updating to match new version of source page) |
(Updating to match new version of source page) |
||
| Line 1: | Line 1: | ||
<languages /> | <languages /> | ||
'''QIIME''' ( | '''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. | ||
'''Note''': QIIME 2 has | '''Note''': QIIME 2 has replaced 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 have a [https://www.anaconda.com/ conda] environment. | |||
===With 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 | 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 [https://docs.qiime2.org/ here]. Instructions adapted for Compute Canada systems are given here 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. | |||
<pre> | <pre> | ||
eb Miniconda3-4.5.12.eb | eb Miniconda3-4.5.12.eb | ||
| Line 23: | Line 22: | ||
conda activate qiime2-2019.7 | conda activate qiime2-2019.7 | ||
</pre> | </pre> | ||
Remember to log out and back in after "conda init bash" step. | Remember to log out and log back in after the "conda init bash" step. | ||
To use | To run QIIME 2, use | ||
<pre> | <pre> | ||
module load miniconda3 | module load miniconda3 | ||
| Line 31: | Line 30: | ||
</pre> | </pre> | ||
===Without conda environment (preferred)=== | ===Without a conda environment (preferred)=== | ||
Since we know that conda environments can create more problems that | 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, use | ||
<pre> | <pre> | ||
eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb | eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb | ||
</pre> | </pre> | ||
This | This takes a while, but will provide you with the qiime/2019.7 module that you need to load before using QIIME 2. | ||
<pre> | <pre> | ||
module load qiime2/2019.7 | module load qiime2/2019.7 | ||
</pre> | </pre> | ||
= | =References = | ||
[http://qiime.org/ QIIME homepage]<br> | [http://qiime.org/ QIIME homepage]<br> | ||
[https://easybuild.readthedocs.io/en/latest/ | [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> | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
[[Category:User Installed Software]] | [[Category:User Installed Software]] | ||