Demultiplexing barcoded/indexed reads with Novobarcode

Novobarcode may be used to separate Illumina reads based on a sequence tag or index. These are also referred to as barcodes.
The process is known as demultiplexing.

To use novobarcode on barcoded reads run the following:

novobarcode -b tags.txt -f s_2_2_0001_qseq.txt s_2_2_0002_qseq.txt -F QSEQ

and output is fastq format.

Novobarcode can also output qseq format:

novobarcode -b tags.txt -f s_2_2_0001_qseq.txt -i s_2_2_0002_qseq.txt -F QSEQ

Note that you need to use the -i option if doing paired end qseq with three read files. Here's an example run report... <

# novobarcode (Beta-0.7) - Tagged Read Classifier.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# License file: /home/sparks/bin/novoalign.lic  
# Licensed to Novocraft Technologies Internal Use Only  
#  novobarcode -b tags.txt -f s_2_2_0001_qseq.txt s_2_2_0002_qseq.txt -F QSEQ 
# Starting at Tue Oct 18 09:51:24 2011 
# Opening barcode tag file 'tags.txt'...  
# Closing tag file.  
# Distance 3  
# Format N 5 
ID    Tag    Count  
2    ACAGTGA    0  
1    CGATGTA    2  
3    TGACCAA    3 
NC    NC    3 
# Finished at Tue Oct 18 09:51:24 2011

More information is available from the  Novobarcode User guide.