Re: [galaxy-dev] Alternative bowtie tools

On Tue, Mar 29, 2011 at 1:31 AM, Assaf Gordon <gordon@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