[EMBOSS] SAM format

Peter Rice pmr at ebi.ac.uk
Thu Jan 20 09:36:00 UTC 2011

On 01/20/11 09:06, Stephen Taylor wrote:
> Hi Peter,
>>> Is EMBOSS planning to release tools that produce SAM format in the near
>>> future or is it more likely to be on the customary July 15th release?
>> The last release EMBOSS 6.3.1 has SAM as an output format for sequences
>> and pairwise alignments (-oformat sam and -aformat sam respectively).

... oops, -osformat for sequences of course.

> Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that
> due to be supported?

Ah, fuzznuc reports features so we hadn't implemented SAM there.

However, you can use -rformat listfile to get USAs for the features, and 
then seqret -osformat sam @listfilename to get the sequences in SAM format.

Possibly scope to do more there. What would you like to see in SAM 
output for fuzznuc?



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