Assemble prokaryotic and eukaryotic reads using the HipMer assembly pipeline.
KBase wrapper for the HipMer Assembler (v18.104.22.168).
HipMer is a high performance parallelization and port of Meraculous ( http://jgi.doe.gov/data-and-tools/meraculous/ ). It is largely written in UPC, with the exception of the UFX generation, which is written in C++/MPI.
For more details see: https://sourceforge.net/p/hipmer/wiki/Home/
This project is a joint collaboration between UC Berkeley ( http://www.eecs.berkeley.edu ), JGI ( http://jgi.doe.gov ), and CRD ( http://crd.lbl.gov/ )
Primary authors are: Evangelos Georganas, Aydin Buluc, Steven Hofmeyr, Leonid Oliker and Rob Egan, with direction and advice from Kathy Yelick. The original Meraculous was developed by Jarrod Chapman, Isaac Ho, Eugene Goltsman, and Daniel Rokhsar.
- Georganas, Evangelos, et al. "HipMer: an extreme-scale de novo genome assembler." Proceedings of | the International Conference for High Performance Computing, Networking, Storage and Analysis. ACM, 2015. ,
- J. A. Chapman, I. Ho, S. Sunkara, S. Luo, G. P. Schroth, and D. S. Rokhsar, "Meraculous: De novo | genome assembly with short paired-end reads," PLoS ONE, vol. 6, no. 8, p. e23501, 08 2011. ,
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