SPAdes¶

SPAdes, Saint-Petersburg genome assembler, is an assembly toolkit containing various assembly pipelines. The bundle packages version 4.1.0.

Usage example¶

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

1	`module load spades`

The SPAdes pipelines can be run as shown as below:

coronaspades.py
metaplasmidspades.py
metaspades.py
metaviralspades.py
plasmidspades.py
rnaspades.py
rnaviralspades.py
spades-gbuilder
spades-gfa-split
spades-gmapper
spades-gsimplifier
spades-kmercount
spades-kmer-estimating
spades.py
spades-read-filter
truspades.py

The spades_shell command can be used to access a shell in the bundle.

1	`spades_shell`

Performance notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

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