On Tue, Mar 29, 2011 at 1:31 AM, Assaf Gordon <gor...@cshl.edu> wrote:
> Hello all,
>
> We're developing alternative bowtie tools that more closely suit our
> needs, are we're happy to share (and get comments).
>
> The main differences are:
> 1. separate tools for paired-end and single-end

Sounds sensible to me.

> 2. the tools accepts FASTA, FASTQ in both Sanger and Illumina
> format (no more need for grooming). Illumina is the default for
> newly uploaded FASTQ files.

I think that's a bad idea - use Sanger FASTQ as the default to be
consistent with the rest of Galaxy, and also with CASAVA 1.8
Illumina machines will produce that too, see:
http://seqanswers.com/forums/showthread.php?t=8895

Peter
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