sga by jts

experimental de novo sequence assembler using string graphs

SGA is a de novo sequence assembler based on the assembly string graph [1]. It is implemented as a collection of algorithms based on the FM-index/Burrows-Wheeler transform. This includes the efficient FM-index to string graph construction algorithm described in [2]. The package also contains programs to correct sequencing errors and remove duplicate reads without using a reference genome.

Dependencies

google-sparsehash (http://code.google.com/p/google-sparsehash/)
zlib (www.zlib.net)

License

GPLv3

References

E.W. Myers. The fragment assembly string graph. Bioinformatics. 21(suppl_2):ii79–85, 2005. [Pubmed]
J.T. Simpson, R. Durbin. Efficient construction of an assembly string graph using the FM-index. Bioinformatics, 26(12):i367-373, 2010. [Pubmed]

Authors

Jared Simpson (js18[-at-]sanger.ac.uk)

Download

You can download this project in either zip or tar formats.

You can also clone the project with Git by running:

$ git clone git://github.com/jts/sga