General info:

This is the read me document that will explain the process of moving through the GBS pipeline to find single nucleotide polymorphisms or SNP's. This is a four step pipeline so I will be breaking the tutorial up into four different sections, one per function. They will be available on the knowpulse website. Links will be provided to the previous function and the next function from the current step you are working on. Prior to starting the pipeline I strongly recommend that you look through and try to understand the concepts behind each step of the process. Below is a flowchart of said concepts and a small description of each step.

 (A) De-multiplex samples: Raw paired-end Illumina reads are assigned to a sample using barcode sequences, which are subsequently trimmed. (B) Trim and filter reads: De-multiplexed paired-end reads are trimmed for base quality and Illumina adaptors. (C) Align reads to a reference genome. (D) Raw SNP calls: Every position in each sample’s alignment is scanned to determine the probability of a variant. (Flowchart and description kindly provided by Carolyn Caron of the University of Saskatchewan Plant Sciences Bioinformatics group)

 For more information on the command line usage of each function please take a look at this link as we will be following a somewhat modified version of the specified commands. 

https://github.com/carolyncaron/GBSpipeline/wiki/GBS-pipeline-POD

The link that I have provided may have some daunting materials within it but don't be discouraged. One of our members has developed a much easier way to work with these commands.

If you have taken a look at the supplied materials and feel ready to start with the pipeline then you can continue on to the tutorial section labelled "Command Line and File Organization"

Below are the links to all of the tutorials involved in the GBS pipeline:

Command Line and File Organization:  http://knowpulse.usask.ca/portal/node/1772322
Friendly Server Usage: http://knowpulse.usask.ca/portal/node/1772323
Step 1 - Demultiplexing: http://knowpulse.usask.ca/portal/node/1772190
Step 2 - Trimming: http://knowpulse.usask.ca/portal/node/1772191
Step 3 - Alignment: http://knowpulse.usask.ca/portal/node/1772192
Step 4 - SNP calling: http://knowpulse.usask.ca/portal/node/1772193