[EMBOSS] ABI to FASTQ with seqret

[Peter]

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.

seqret -sformat abi -osformat fastq-sanger -sequence example.ab1
-outseq example.fastq -auto

Output as FASTA seems fine:

seqret -sformat abi -osformat fasta -sequence example.ab1 -outseq
example.fasta -auto

Is ABI to FASTQ a reasonable to expect seqret to support? If so, could
it be added to the TODO list please?

Peter C.

P.S. I'd be interested to hear suggestions for alternative tools to
tackle this conversion.