Fwd: Bug#692332: ITP: sga -- A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

[Michael Crusoe <michael.crusoe@gmail.com>]

I forgot the have the list own this when I sent this ITP out.

The packags is at git://git.debian.org/debian-med/sga.git with
upstream in master and the package in debian.

Feedback is welcome.

What is the next step to get bamtools and sga into Debian \ BioLinux \
Ubuntu etc..?

---------- Forwarded message ----------
From: Michael Crusoe <michael.crusoe@gmail.com>
Date: Sun, Nov 4, 2012 at 7:20 PM
Subject: Bug#692332: ITP: sga -- A de novo genome assembler based on
the concept of string graphs. The major goal of SGA is to be very
memory efficient, which is achieved by using a compressed
representation of DNA sequence reads.
To: Debian Bug Tracking System <submit@bugs.debian.org>


Package: wnpp
Severity: wishlist
Owner: "Michael R. Crusoe" <mcrusoe@asu.edu>

* Package name    : sga
  Version         : 0.9.35
  Upstream Author : Jared Simpson <js18@sanger.ac.uk>
* URL             : https://github.com/jts/sga
* License         : GPLv3
  Programming Lang: C++
  Description     : A de novo genome assembler based on the concept of
string graphs. The major goal of SGA is to be very memory efficient,
which is achieved by using a compressed representation of DNA sequence
reads.

SGA is a de novo assembler for DNA sequence reads. It is based on Gene
Myers' string graph
formulation of assembly and uses the FM-index/Burrows-Wheeler
transform to efficiently
find overlaps between sequence reads. The core algorithms are
described in this paper:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/i367