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.