Developed by:
Alberto Riva
DiBiG – ICBR Bioinformatics
University of Florida

Demux is a command-line tool to handle barcodes in DNA sequences in FASTA or FASTQ format. Its main function is to separate sequences into different files according to their barcodes. Barcodes can be specified by the user or automatically detected. Other options include trimming the barcodes in output, and matching barcodes at both ends of the sequence.


Demux is distributed as a GNU/Linux command-line 64bit executable. Source code is available upon request.

Download Demux

Demux is also available on HiPerGator, in the dibig_tools module. To use it, execute:

module load dibig_tools


Documentation for Demux is available in this file.

Demux contains an integrated help system. Call

demux -help all

to get a list of command-line options, or

demux -help option…

to get help on one or more options.

A complete interactive manual is available, use

demux -manual

to display it.