[Bioperl-l] Next-gen modules

[Chris Fields]

On Jul 8, 2009, at 10:57 AM, Peter Rice wrote:

> Giles Weaver wrote:
>> I've just added a sequence adapter removal implementation to the  
>> bioperl
>> scrapbook at http://www.bioperl.org/wiki/ 
>> Removing_sequencing_adapters. I
>> think the basic method is sound, but the implementation is ugly.
>
> Ugly perhaps, but I'll look anyway :-)
>
> I see you don't use needle because it creates gapped alignments, but
> that can be fixed with a sufficiently high gap penalty (just to see if
> it works - it won't be fast).
>
> We also have word-based matching methods in EMBOSS but they would not
> allow mismatches. I will play with alternatives and see what works  
> best.
> Some word-based seed should allow for a faster solution.
>
> The provisional EMBOSS name for a quality filter and adaptor removal
> application is "quaffle"
>
> regards,
>
> Peter Rice

In the meantime, we can probably add this in to Bio::SeqUtils for  
general use as an exported method.

It would be nice to get some regression tests going for this to make  
sure it does what we expect, so maybe some test data and expected  
results?

chris