[EMBOSS] ABI to FASTQ with seqret

Peter Rice pmr at ebi.ac.uk
Thu Apr 22 15:22:01 UTC 2010

On 22/04/2010 16:06, Peter C. wrote:

> Hello again Peter R (&  everyone else at EMBOSS),
> Did you manage to find out if the PCON confidence values in ABI files
> are PHRED quality scores or not?

Yes ... and maybe.

The first scores are written bu the ABI basecaller.

A second set can be written by any basecaller. These may be phred quality 
scores but could in theory be anything.

EMBOSS will assume they are phred scores as there is no way to tell otherwise.


Peter Rice

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