[EMBOSS] Conservation of FASTQ scores by the EMBOSS tools.

Peter biopython at maubp.freeserve.co.uk
Wed Sep 16 09:31:22 UTC 2009

On Wed, Sep 16, 2009 at 7:57 AM, Charles Plessy
<charles-listes-emboss at plessy.org> wrote:
> Dear EMBOSS developers,
> I have multi-sequence file in FASTQ format that contains sequencing reads, and
> would like to retreive them the with seqret. But as you see in the following
> example, quality scores are not preserved:
> $ seqret P13-CA.fq:F1EZY7316JY25B fastq::stdout
> Reads and writes (returns) sequences
> @F1EZY7316JY25B rank=0000040 x=3973.0 y=285.0 length=68
> +
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

You need to use "fastq-sanger" (or the other variants), since in
EMBOSS, "fastq" currently means FASTQ ignoring the qualities.
This is documented:


As an EMBOSS user, I think the current situation is confusing, and
it would make much more sense to have "fastq" just an alias for
"fastq-sanger" (which would be consistent with Biopython and BioPerl).


And also this email - especially the last example:

> The purpose was to use seqret as a workaround for the fact that
> vectorstrip does not keep the quality either.

That's also been suggested, and is likely to be supported in future.


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