MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. 


  • MEGAHIT wiki 
  • MEGAHIT on Gitlab
  • If you use MEGAHIT in your research, please cite: 
    • 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 [PMID: 25609793].
    • Li, D., Luo, R., Liu, C.M., Leung, C.M., Ting, H.F., Sadakane, K., Yamashita, H. and Lam, T.W., 2016. MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Methods.



To see what versions of MEGAHIT are available type

module avail megahit

To see what other modules are needed, what commands are available and how to get additional help type

module help megahit

To use MEGAHIT, include a command like this in your batch script or interactive session to load the megahit module:

module load megahit

Be sure you also load any other modules needed, as listed by the module help megahit command.