[EMBOSS] Convert scf to fasta

Peter Rice pmr at ebi.ac.uk
Mon Apr 26 14:10:44 UTC 2010

Dear Phil,

On 26/04/2010 13:47, Philip H. Jones 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.

We can read .abi files (we have some extensions for the next release to 
cover abi format in more detail).

I will pick up some scf files and check what the difference is. We have 
not tried them before.

Any other formats we can usefully cover?


Peter Rice

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