[EMBOSS] ABI to FASTQ with seqret

[Peter Rice]

On 30/03/2010 14:13, Peter Rice wrote:

> Where do I look to find scores that we can use (and how do we convert
> those to phred quality scores)?

Aha, found something. The field is called PCON (confidence values), with 
values 0-255.

There is a possibility that these could be phred scores, but I suspect they 
are whatever the basecaller has decided to write there.

http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf

Peter R.