Scripts - Analyses and Parameters

All QIIME analyses are performed using python (.py) scripts, which are located in the your QIIME scripts directory. To access QIIME python scripts, this directory should be in your $PATH environment variable. You should have set this up during installation (unless you’re using the virtual box, in which case it was already set up).

You can then call QIIME scripts as:

python align_seqs.py -h

All QIIME scripts can take the -h option to provide usage information.

An index of the QIIME scripts is provided here.