Barcoded Data Preparation Tools Documentation

This page contains the most recent version of our barcoded data preparation tools, the following describes the included scripts and information on proper usage.

Meric Lieberman, 2016
This work is the property of UC Davis Genome Center – Comai Lab. This is shared under a Creative Commons BY-NC-ND 4.0 license.

Use at your own risk. We cannot provide support. All information obtained/inferred with these scripts is without any implied warranty of fitness for any purpose or use whatsoever.


The scripts included are for use in preparation of raw illumina reads for further analysis.

Traditionally, we do all prep work with a single script called “Allprep”, that does barcode/index check and match, 
‘N’ filtering, primary and secondary adapter contamination, quality conversion, quality trimming, 
length trimming, and library separation.

However, if parts of the preparation process needs to be performed independently, we also provide smaller scripts to do the process modularly. 

Allprep now is capable of one performing barcode/index splitting without any trimming or read filtering, please see README for run details.

Please note that:

  1. All of the scripts have a description of what they do, input parameters, and running directions at the beginning of each program. 
  2. All scripts use command line parameters as input and all scripts can be run with ./”program_name” provided Python 2.6+ is installed on your system. 
  3. These scripts can be used with paired end or single ended data, and some can be run on data without barcodes.

On a unix based system, get the most current package from github, then use the command “unzip” if not cloning it. 

A new folder called barcoded_data_toolbox will appear, with all of the scripts and the README.txt inside. The README has all of the information here, as well as run parameters for all scripts.


This .tgz includes: - Single script to do all processing as detailed above. - This script will interleave two files or uninterleave a file. This is only applicable to paired-end reads. "Interleaved" means that the two ends of a read are placed together in the final file. View parameters in script for running directions.

%d bloggers like this: