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Old 07-04-2013, 06:58 AM   #2
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Location: uk

Join Date: Mar 2009
Posts: 667
Default Velvet + meta-velvet:which fastq format for paired-end infos?

I have been using velvet with the new formats of MiSeq and HiSeq PE data, and it works fine.

By the way, in the read that you have used to illustrate the new format, the Y (1:Y:18:ATCACG) indicates a read that has not passed Illumina's QC filter step.

Usually the sequence providers remove those reads.
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