Mapping short sequencing reads to distant relatives
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
AcoSeeD: an ant colony optimization for finding optimal spaced seeds in biological sequence search
ANTS'12 Proceedings of the 8th international conference on Swarm Intelligence
Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Design and analysis of periodic multiple seeds
Theoretical Computer Science
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Summary: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures. Availability: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/. Contact: shrimp@cs.toronto.edu Supplementary information:Supplementary data are available at Bioinformatics online.