[EMBOSS] ABI to FASTQ with seqret

[Peter Rice]

On 30/03/2010 12:46, Peter wrote:
> Hi all,
>
> I've got some "Sanger" capillary sequence files in ABI trace file
> format, which I understand includes the probabilities of the 4 bases
> along the sequencing run. I'd like to extract this as a FASTQ file
> with meaningful quality scores based on the trace data (for use in
> assembly).
>
> This doesn't seem to work - the FASTQ quality score characters are all
> double quotes (ASCI 34), meaning PHRED quality 1.

We have code to extract various fields from ABI trace files, but I'm not 
familiar with the details fo the format, and documentation appears hard to 
find.

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

regards,

Peter