What it does

This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but the threshold and window size can be adjusted.

The process_radtags program can:

• handle data that is barcoded, either inline or using an index, or unbarcoded.
• use combinatorial barcodes.
• check and correct for a restriction enzyme cutsite for single or double-digested data.
• filter adapter sequence while allowing for sequencing error in the adapter pattern.
• process individual files or whole directories of files.
• directly read gzipped data
• filter reads based on Illumina's Chastity filter

Help

Input files:

• A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list)
• Barcode File

The barcode file is a very simple format:

Combinatorial barcodes are specified, one per column, separated by a tab:

The sample name column can be omitted. Then the Barcodes are used for naming the output files.

Created by:

Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko

Project links:

Stacks website

Stacks manual

Stacks google group