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