LightStringGraphs (LSG) is an external memory string graph construction tool.
It allows to use only limited RAM to assemble a genome from very large NGS datasets. We developed a new startegy to use the FM-index for finding the overlaps between all pairs of reads.
References
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi: Constructing String Graphs in External Memory. WABI 2014: 311-325. 2014. http://dx.doi.org/10.1007/978-3-662-44753-6_23. slides
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi: Constructing String Graphs in External Memory. arXiv:1405.7520
Downloads and support
Please refer to the project page for downloads, instructions and support.
The software is freely available under GPLv3 license.