taskSavannah Administration - Tasks: task #7778, Submission of myrialign

 
 

task #7778: Submission of myrialign

Submitter:  Paul Harrison <pfh>
Submitted:  Mon 18 Feb 2008 09:53:11 PM UTC
   
 
Should Start On:  Mon 18 Feb 2008 12:00:00 AM UTC Should be Finished on:  Thu 28 Feb 2008 12:00:00 AM UTC
Category:  Project Approval Priority:  * 5 - Normal
Status:  Done Privacy:  Public
Assigned to:  mjflick Open/Closed:  Closed
* Mandatory Fields

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Tue 19 Feb 2008 12:53:47 AM UTC, comment #1: 

Hi,

I have approved your project.  You will receive an automated e-mail containing detailed information about the approval.

Regards.

Michael J. Flickinger <mjflick>
Mon 18 Feb 2008 09:53:11 PM UTC, original submission:  

A new project has been registered at Savannah
This project account will remain inactive until a site admin approves or discards the registration.


Registration Administration


While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific Group Administration page, accessible only to site administrators, effectively logged as site administrators (superuser):



Registration Details


  • Name: myrialign
  • System Name:  myrialign
  • Type: non-GNU software & documentation
  • License: GNU General Public License v3 or later





Description:

This is bioinformatics software to align short reads produced by a short read genome sequencer to a reference genome. It can use a Cell Broadband Engine to accellerate alignments if available, for example on a PlayStation 3 running GNU/Linux.

A sequencing run might produce several million short reads. A typical next step is to align all of these reads to a reference genome, to see what differences exist: Single Nucleotide Pair changes, insertions, and deletions.

Myrialign performs brute force Smith-Waterman alignment using a variant on the "bitap" algorithm that aligns several thousand reads in parallel. It uses bit-parallelism, multiple processors, and Cell SPUs if available.

Unlike other reference genome alignment software, heuristics and hashtable lookups are not used. Myrialign will find alignments with any number of errors up to a user specified cutoff. The emphasis is on doing full Smith-Waterman alignment fast.


Tarball URL:

http://www.logarithmic.net/pfh-files/random/myrialign-0.1.tar.gz


Paul Harrison <pfh>

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

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  • -email is unavailable- added by mjflick (Posted a comment)
  • -email is unavailable- added by pfh (Submitted the item)
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    Follow 3 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2008-02-19 mjflick StatusNone Done
        Assigned toNone mjflick
        Open/ClosedOpen Closed

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