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QIIME Scripts

All QIIME analyses are performed using python (.py) scripts. See the QIIME install guide if you need help getting the QIIME scripts installed.

All QIIME scripts can take the -h option to provide usage information. You can get this information for the align_seqs.py script (for example) by running:

align_seqs.py -h

The same documentation that is presented when calling a script with -h is available for all QIIME scripts at the links below.

QIIME script index

biom-format scripts

Scripts in the biom-format project provide functionality for working with biom tables generated in QIIME.

Other documentation of the biom-format project can be found at www.biom-format.org.

biom-format is a dependency of QIIME, so these scripts should already be available in your QIIME environment.

emperor scripts

Scripts in the emperor project provide functionality for generating interactive 3D ordination plots from QIIME ordination results.

Other documentation of the emperor project can be found at biocore.github.io/emperor.

emperor is a dependency of QIIME, so these scripts should already be available in your QIIME environment.

PICRUSt scripts

Scripts in PICRUSt provide functionality for performing predictive metagenomics, and for normalizing closed-reference OTU tables by 16S copy number.

See the PICRUSt script index.

Other documentation of PICRUSt can be found at picrust.github.io/picrust


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