MetaHipMer Version 2.0
July 27, 2022: a bug fix patch to support building with newer compilers was released 18.104.22.168.
January 24, 2022: a new release, version 2.1.0, is available. Several stages now can take advantage of Nvidia GPUs, with significant performance improvements on systems with GPUs (e.g. up to 4.5x at scale on the Summit supercomputer). What's new in this release can be seen here. For details on how to install and run MHM2, please consult the User guide.
MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and CUDA, and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes. More information about MetaHipMer can be found in:
- E. Georganas et al., "Extreme Scale De Novo Metagenome Assembly," SC18: International Conference for High Performance Computing, Networking, Storage and Analysis, Dallas, TX, USA, 2018, pp. 122-13.
- Hofmeyr, S., Egan, R., Georganas, E. et al. Terabase-scale metagenome coassembly with MetaHipMer. Sci Rep 10, 10689 (2020).
Quality of MetaHipMer assemblies is comparable with other leading metagenome assemblers, as noted in the results of the CAMI2 competition, where MetaHipMer was rated first for quality in two out of three datasets, and second in the third dataset:
- F. Meyer et al., "Critical Assessment of Metagenome Interpretation: the second round of challenges", Nature Methods volume 19, pages429–440 (2022)
MHM2 is developed and maintained by the Exabiome Project at Lawrence Berkeley National Laboratory, and is supported by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration.
Releases of MetaHipMer prior to Version 2 can be found at the HipMer download page.