[Bioperl-l] Next-gen modules

[Mark A. Jensen]

Thanks Elia for those wiki notes--
[I would say you received an enthusiatic 'welcome back'!]
cheers, 
Mark
----- Original Message ----- 
From: "Elia Stupka" <e.stupka at ucl.ac.uk>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, June 17, 2009 3:37 PM
Subject: Re: [Bioperl-l] Next-gen modules


> 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
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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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>