[Bioperl-l] Creating a fastq format file?

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Sun Apr 26 01:50:14 EDT 2009

> > This might be a good place to ask the question: having looked at the
> > fastq.pm page, is the fastq format defined (only) by a "@'" followed by
> a
> > sequence line and a "+" header followed by a quality line and the two
> > headers have to agree? Now that Illumina is using phred scaling, are
> > 'Sanger' and 'Illumina' versions the same?
> No they aren't the same, Illumina still encodes the ascii as value + 64
> and Sanger as value + 33.

Illumina have now CHANGED how they calculate the quality value however in
the last month or so... Their Q range used to be -5..40 mapped to ASCII 64+,
but now they produce Q >= 0 and it is unclear if they start at 69 or 64

I have tried to summarise this in a central place:


Corrections welcome!

--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA

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