<p>I have fastq file with undetermined reads from Illumina HiSeq. The reads in fastq file contains illumina barcode. I do now know what barcode has been used in the lab and there is no way i could find it out. Is it possible to find it out from the fastq file I received. Are there any tools that show most repeated sub-sequence in each reads of fastq file ?</p>

<p><strong>[14-01-2014] Edit1:</strong>
I have ilumina base call files (raw data from sequencer). I have possibility to convert .bcl files to .fastq using bcl2fastq provided by Illumina.</p>

<p>Assuming the demultiplexing was carried out specifying the index sequence location, then this could be used:</p>

<p><code>grep ^@HISEQ lane1_Undetermined_L001_R1_001.fastq | cut -d":" -f10 | uniq -c | sort -nr &gt; barcodes.txt</code></p>

<p>This outputs a text file containing every barcode in the FASTQ file, with a count of how many times it is seen.  The most frequent is at the top of the list.  Could help you find the barcode?</p>
