On Thu, Feb 10, 2011 at 6:42 PM, Peter wrote:
> On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor wrote:
>> Sounds like this should be added into the main release. It would save a lot
>> of time/disk space instead of using Groomer.
> I agree. Maybe Dan can take care of it - I don't have bowtie setup
> on our local Galaxy (yet) so I wouldn't be able to test the proposed
> fix.
> In the long term however the Solexa/Illumina FASTQ formats are on
> their way out since CASAVA 1.8 will switch to the Sanger FASTQ
> encoding: http://seqanswers.com/forums/showthread.php?t=8895

Hi Stephen,

Maybe you should file an issue on bitbucket about extending the Bowtie
wrapper to support fastqillumina as well as fastqsanger as input?

The current version of the wrapper is here if you want to look at it:

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