Qiime Guide

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Qiime Bioinformatics Package Guide (in progress)

Qiime is a set of bioinformatics software packages and scripts that allows users to process, analyze, and interpret 16S rRNA sequencing datasets. It is

This guide assumes that the user is already familiar with the basic operation and scripts of Qiime and only covers issues regarding running Qiime on the HPC Cluster. For more information about Qiime and the tools and analyses available, please see the Qiime Homepage.


Loading Qiime

Before using Qiime, users must load the Qiime module as follows:

  module load Qiime/1.50

This will load the base Qiime package, Python 2.7.1, and nearly all dependency packages.

Usage notes

There are two primary ways of using Qiime on the cluster. The first is intereactively, in a manner similar to how one would use Qiime on their own computer. The second is in a batch mode where the user supplies sequential Qiime commands in a job script that is submitted to the job handler for processing. Users are encouraged to use the batch method.

Interactive mode

To use Qiime interactively on the cluster, users must first logon on to the cluster with X11 forwarding enabled. To achieve this, please consult __HELP__.

When properly logged on, users who wish to use Qiime interactively will need to use the command: XXXXX

Batch mode

The preferred method of using Qiime on the cluster is with a batch script where multiple Qiime commands are sequentially processed by the job handler. To achieve this the user must first create a plain text job file indicating BLAH BLAH BLAH.