[Bioperl-l] Conversion of Phred 33 -> Phred 64 quality

Fields, Christopher J cjfields at illinois.edu
Mon Jan 26 15:16:41 UTC 2015

This would be the so-called fastq-illumina’ or ‘fastq-solexa’ variants.  FASTQ does handle these but the output for modern Illumina pipelines is to generate Sanger-based FASTQ.  

Bio::SeqIO::fastq can interconvert these but it’s painfully slow last time I checked (mainly in part to the underlying sequence quality classes).  They’re not really designed for tons of data and needs refactoring to deal with large sequence data sets.  Lately, frankly, I’ve been using non* methods for doing this, namely seqtk:



> On Jan 26, 2015, at 8:23 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
> Hi folks,
> I know I could RTFM, but maybe someone knows off the top of their head: I understand that Illumina at one time made a switch in the constant added to quality scores to generate the FASTQ that comes off their instruments. This leads to a certain incomparability of data before and after that switch. This is about all I know of the issue; does anyone here have experience with this? Are there any BP modules that do this translation?
> much appreciated-
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list