[Bioperl-l] Next-gen modules
tristan.lefebure at gmail.com
Wed Jun 17 09:27:12 EDT 2009
Regarding next-gen sequences and bioperl, following my
experience, another issue is bioperl speed. For example, if
you want to trim bad quality bases at ends of 1E6 Solexa
reads using Bio::SeqIO::fastq and some methods in
Bio::Seq::Quality, well, you've got to be patient (but may
be I missed some shortcuts...).
A pure perl solution will be between 100 to 1000x faster...
Would it be possible to have an ultra-light quality object
with few simple methods for next-gen reads?
I can contribute some tests if that sounds like an important
On Wednesday 17 June 2009 08:02:11 Mark A. Jensen wrote:
> I say a definite +1; in fact, this sounds like it should
> be a Hot Topic (see
> http://www.bioperl.org/wiki/Category:Hot_Topics for some
> others you might have missed in your hiatus...). I will
> create a page that can be a central point for wish lists,
> discussion, etc.
> There has been much discussion of late about FASTQ
> cheers from a newbie,
> ----- Original Message -----
> From: "Elia Stupka" <e.stupka at ucl.ac.uk>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, June 17, 2009 7:29 AM
> Subject: [Bioperl-l] Next-gen modules
> > Dear all,
> > after several years of absence I am slowly coming back
> > to Bioperl, and hope to contribute again to its
> > development.
> > One area that I was thinking of starting from, since we
> > are actively involved with it, is to improve BIoperl's
> > support fo next-gen sequencing data, tools, etc. Since
> > I am sure I have missed out on a lot of recent
> > developments, do let me know if/what is useful.
> > One example that comes to mind is that the conversion
> > of various formats to/from FASTQ does not seem to be
> > supported. Some code can be found within Li Heng's
> > script: http://maq.sourceforge.net/ fq_all2std.pl but
> > it would be good if it could make its way into SeqIO?
> > And similarly, potentially, for other next-gen sequence
> > formats?
> > Similarly, there seems to be little in bioperl-run to
> > support tools that have been developed in this area,
> > such as Maq, BowTie, TopHat, etc?
> > Do let me know if there is a past thread on this, or
> > other people actively developing, etc. so that I can
> > find out what priorities are.
> > thanks and best regards to all (old friends and new),
> > Elia
> > ---
> > Senior Lecturer, Bioinformatics
> > UCL Cancer Institute
> > Paul O' Gorman Building
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