[Bioperl-l] Next-gen modules
e.stupka at ucl.ac.uk
Wed Jun 17 08:54:22 EDT 2009
thanks a lot for the pointers.
With regards to FASTQ parsing:
-my understanding by reading past threads is to work on a single
format, i.e. FASTQ and to interpet the quality "flavours" as just
quality conversions, right?
-However, I assume we would still want to support a simple way for the
user to say format => 'fastq-solexa' using the nomenclature adopted in
BioPython suggested by Peter, right?
-I also saw Heikki's "long essay", but did not yet compare to Heng
Li's code at http://maq.sourceforge.net/fq_all2std.pl, I guess we
would hope they would produce identical outputs, will be a good check.
Finally, I saw Tristan's reply to Heikki's thread, so what is the
status quo? Is it moving forward?
On 17 Jun 2009, at 13:02, 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
> 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 http://lists.open-bio.org/pipermail/bioperl-l/2009-June/030187.html
> cheers from a newbie, Mark
> ----- 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
>> 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),
>> Senior Lecturer, Bioinformatics
>> UCL Cancer Institute
>> Paul O' Gorman Building
>> University College London
>> Gower Street
>> WC1E 6BT
>> Office (UCL): +44 207 679 6493
>> Office (ICMS): +44 0207 8822374
>> Mobile: +44 7597 566 194
>> Mobile (Italy): +39 338 8448801
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
Senior Lecturer, Bioinformatics
UCL Cancer Institute
Paul O' Gorman Building
University College London
Office (UCL): +44 207 679 6493
Office (ICMS): +44 0207 8822374
Mobile: +44 7597 566 194
Mobile (Italy): +39 338 8448801
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