[EMBOSS] ABI to FASTQ with seqret

Peter biopython at maubp.freeserve.co.uk
Thu Apr 22 15:48:29 UTC 2010

On Thu, Apr 22, 2010 at 4:22 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
> 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.
> regards,
> Peter Rice

Does this mean there is an updated seqret in a public repository where I
can convert an ABI file to FASTQ taking the ABI basecaller's sequence
and PHRED scores? I'd be interested to test that... or a patch against
EMBOSS 6.2.0.


Peter C.

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