[EMBOSS] ABI to FASTQ with seqret

[Peter]

On Tue, Mar 30, 2010 at 1:02 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
> On 30/03/2010 12:46, Peter C. 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.
>
> I will take a look. I don;t recall anyone using the quality scores from ABI
> data when we first imeplemented it (at that time Staden Experiment files
> were the only supported output format with any quality scores)
>

Thanks Peter,

Regarding other possible tools, there is the obvious choice of
PHRED (although getting a copy is non-trivial), and based on
this thread: http://seqanswers.com/forums/showthread.php?t=3165
I've just tried TraceTuner 3.0.6beta which is open source
(specifically, GPL v2 or later):
https://sourceforge.net/projects/tracetuner/

With the ttuner -nocall option to reuse the sequence as-is from
the ABI file results in zero quality scores.

Allowing ttuner to re-call the bases (the default), it can output
FASTA/QUAL/PHD with meaningful qualities (from which I can
easily make a FASTQ file).

Peter C.