Why use this pipeline?

There are several complete pipelines that are well maintained and coumented; the two most popular being Mothur and Qiime, with DADA2 and deblur gaining a lot of popularity recently. So there are many options. Mothur runs in its own environment; it has linear workflows and does not allow you to change the input/output file names. This can be confusing for users interested in intermediate steps of the workflow. Qiime is better about this; it is run using Python but hsa very fickle input requirements that can lead to a lot of lost time.

This pipeline was originally created by Fan Yang in the GERMS-lab. The purpose is that it allows much more control over every step, and is very transparent in how its workflow. She periodically updates her pipeline, but I maintain my own version that I will update and annotate here.

Files

• Sequence Files
• Reference Database
• Mapping Files

Your Shell Environment

• Paths to Your Data
• Paths to Programs
• Sequence Read Parameters
• Cores

Read Processing

• Pair-End Read Assembly
• Read Quality Filter
• Demultiplexing
• Create Master Read File

Chimera Removal

• Dereplicating and Sorting Reads
• Chimera Detection
• Sort for Clustering

OTU Calling

• Clustering
• Sample Mapping
• Taxa Classification

HPCC

Pipeline

Questions

If you have any questions, feel free to contact me by e-mail at sdsmith@iastate.edu