[Bioperl-l] Creating a fastq format file?

[Torsten Seemann]

> > 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
now...

I have tried to summarise this in a central place:

http://en.wikipedia.org/wiki/FASTQ_format

Corrections welcome!


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