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>]

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