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SPAdes

SPAdes, Saint-Petersburg genome assembler, is an assembly toolkit containing various assembly pipelines. The spades bundle packages version 3.15.5.

UFS HPC Usage Example

The following command can be executed in the terminal to load the bundle:

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module load spades
The spades pipelines can be run as shown as below: 
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spades.py
truspades.py
coronaspades.py
plasmidspades.py
rnaspades.py
rnaviralspades.py
metaplasmidspades.py
metaspades.py
metaviralspades.py
The spades_shell commmand can be used to access a shell in the spades bundle. 
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spades_shell

Performance Notes

No performance notes available

No recommended resources available

Benchmarks

No benchmarks available.

UFS HPC Community Guides and Tutorials

  • No community guides available.

Official site and documentation

Licensing Information

SPAdes is licensed under the GPL2 license.

Primary citation

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