[Bioperl-l] Next-gen modules

Peter Rice pmr at ebi.ac.uk
Wed Jul 8 15:57:47 UTC 2009

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"


Peter Rice

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