MEGAHIT

MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

MEGAHIT is made available on the UFS HPC via a conda environment which can by loaded as a module.

UFS HPC Usage Example

Follow these steps to use MEGAHIT:

1. Start a qwiz or qvnc session. If using a qvnc session, open the Terminal.

2. Load the MEGAHIT module (current version is 1.2.9):

$ module load life-sciences/megahit

3. Initialize the MEGAHIT environment:

$ megahit_init

4. MEGAHIT can now be executed as advertised.

Performance Notes

The following flags should be set according to the resources requested a particular job:

• The -t flag should be set to the number of cores requested for the job

Recommended resources per session

• 1 Node
• Memory and number of cores will depend on dataset size

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

• No community guides are available.

Official site and documentation

• Site
• Manual

Licensing Information

• MEGAHIT is free to use and distribute under the terms of the GNU General Public License v3.0

Primary citation

• Li, D., Liu, C. M., Luo, R., Sadakane, K., & Lam, T. W. (2015). MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31(10), 1674-1676.

• Li, D., Luo, R., Liu, C. M., Leung, C. M., Ting, H. F., Sadakane, K., ... & Lam, T. W. (2016). MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102, 3-11.

Please remember to cite any additional methods used.

External Guides and Resources

• If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za