Assemble metagenomic reads using the MetaHipMer assembly pipeline.
MetaHipMer is a de novo metagenome short-read assembler capable of scaling up to coassemble terabase-sized metagenomes. This is the KBase App for the second version of the MetaHipMer Assembler (v2.1.0.1-357).
MetaHipMer is a high performance parallelization and port of Meraculous. Version 2 (MHM2) is written entirely in UPC++ and CUDA, and runs efficiently on both single servers and on multi-node supercomputers.
For more details see full documentation for MetaHipMer at: https://bitbucket.org/berkeleylab/mhm2/wiki/Home.md
This project is a joint collaboration between UC Berkeley, JGI, and CRD.
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.
Related Publications
- Hofmeyr Steven, et al. "Terabase-scale metagenome coassembly with MetaHipMer." Sci Rep. 2020 Jul 1;10(1):10689. , https://doi.org/10.1038/s41598-020-67416-5
- 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. ,
App Specification:
https://github.com/kbaseapps/kbase_hipmer/tree/538ffad4a25b69ed119091b753bde6019193701b/ui/narrative/methods/run_hipmer_hpc_metaModule Commit: 538ffad4a25b69ed119091b753bde6019193701b