[Biopython] SeqIO for fasta conversion of Illumina files with > 60 bp

[Peter]

On Tue, Sep 15, 2009 at 8:27 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Just got off the phone with Illumina customer support to double-check this,
> and I think it may be a false alarm, though I'm getting conflicting accounts
> (our local guys say it's solexa, not PHRED qual scores).
>
> According to Illumina tech support, qual scores coming off the 1.4 pipeline
> should be converted over to PHRED scores prior to output (what natassa
> mentions).  The manual refers to the older (Solexa/Illumina 1.0) scoring b/c
> that particular qual scoring option can be specified instead of PHRED.

I gather via seqanswers.com that there are still some (out of date) references
to the old Solexa scoring in the current Illumina pipeline documentation, so I
expect this is just a false alarm...

Peter