Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Parallel and memory-efficient reads indexing for genome assembly
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part II
| Hi-index | 3.84 |
Motivation: Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized. Result: We present a method that eschews the traditional graph-based approach in favor of a simple 3′ extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods. Availability: The software package can be found at http://www.comp.nus.edu.sg/~bioinfo/peasm/. Alternatively it is available from authors upon request. Contact:ksung@comp.nus.edu.sg; sungk@gis.a-star.edu.sg Supplementary information:Supplementary data are available at Bioinformatics online.