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
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.
3. fewer visible options, only the most relevant ones are available (IMHO 
better organized)
4. optional output of non-mappers and maxed-out mappers as FASTQ files (to use 
in downstream analysis or remapping attempts)
5. allows users to to do "quiet" output (only aligned reads are reported in the 
SAM file).
6. allows users to specify custom options (free text field), for those who know 
what they are doing.
7. Outputs a sorted SAM file, and sorting is done using multi-threaded sort.

You can see the interface (but not run the tools) here:

The tools (XML & shell scripts) are available here:

Note about multithreaded bowtie:
currently the tools use 10 threads (hard-coded in the XML files) - easily 

Note about the sorting:
The "sam_sort.sh" script requires the latest sort from coreutils-8.10 (which 
does multi-threaded sort).
The number of threads, maximum amount of RAM allowed for sort, and temporary 
storage directory are all hard-coded in the beginning of the script - easily 

TopHat and Cufflinks tools will follow soon (if there's any interest).

Comments are of course welcomed, these are very much work-in-progress.
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