[EMBOSS] Convert scf to fasta

[Fernan Aguero]

On Mon, Apr 26, 2010 at 9:47 AM, Philip H. Jones
<p.h.jones at liverpool.ac.uk> wrote:
> Hi
>
> I have a large number of .scf files that I need to batch convert to fasta
> format. I thought that abiview would be able to perform this function but I
> cannot get abiview to read the .scf files (although various sources on the
> internet suggest that it should be able to do so). It reads and displays
> .ab1 files with no problems. The webpage describing input formats
> (http://emboss.sourceforge.net/docs/themes/SequenceFormats.html) doesn't
> mention scf. Is there an EMBOSS application that would convert .scf to .fa?
> Any help would be greatly appreciated. I am running Mac OSX 10.5.8 with
> EMBOSS 6.1.0-4 installed via fink.
>
> Best wishes,
>
> Phil Jones

AFAIK, abiview reads trace files but it displays the trace and
sequence data _graphically_. That is to say it's not really meant to
be used for batch conversions.

For this you may want to try phred (free for academic use, see
www.phrap.org, runs on many Unix flavours) or any other basecaller
(don't use OS X myself, can't provide more info on this).

E.g. if you have all your scf files in a directory called 'chromats'
you would run phred like this:
phred -id chromats -sa my-sequences.fasta
to get a multiple fasta file named 'my-sequences.fasta' with the
corresponding sequences.

Note that you have many more options, as phred will also export/report
base quality values for your sequences.

Cheers,

-- 
fernan