SPAdes

SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.

SPAdes 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 SPAdes:

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

2. Load the SPAdes module (current version is 3.15.5):

$ module load life-sciences/spades

3. Initialize the SPAdes environment:

$ spades_init

4. SPAdes 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
• The -m option should be set 2gb below the amount of memory requested for the job. Note that the program will terminate when reaching this value. (Or if unset, the job will crash)

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

• SPAdes is free to use and distribute under the terms of the GNU General Public License v2.0

Primary citation

• Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020). Using SPAdes de novo assembler. Current protocols in bioinformatics, 70(1), e102.

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