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megahit website  

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG construction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (Tesla GPUs no longer available) (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.

Environment Modules

Run module spider megahit to find out what environment modules are available for this application.

System Variables

  • HPC_MEGAHIT_DIR - installation directory
  • HPC_MEGAHIT_BIN - executable directory
  • HPC_MEGAHIT_DOC - documentation directory


If you publish research that uses megahit you have to cite it as follows:

Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/btv033