[Bioperl-l] Next-gen modules

[Elia Stupka]

Dear all,

I tried to summarize today's discussion with what seems to be the  
"shaping consensus" on the Wiki page:

http://www.bioperl.org/wiki/Nextgen_in_Bioperl

good night,

Elia


On 17 Jun 2009, at 13:19, Mark A. Jensen wrote:

> [ and here's a new wikipage: http://www.bioperl.org/wiki/Nextgen_in_Bioperl 
>  ]
> ----- 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
>> University College London
>> Gower Street
>> WC1E 6BT
>> London
>> UK
>> Office (UCL): +44 207 679 6493
>> Office (ICMS): +44 0207 8822374
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>>

---
Senior Lecturer, Bioinformatics
UCL Cancer Institute
Paul O' Gorman Building
University College London
Gower Street
WC1E 6BT
London
UK

Office (UCL): +44 207 679 6493
Office (ICMS): +44 0207 8822374

Mobile: +44 7597 566 194
Mobile (Italy): +39 338 8448801