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SPAdes
Overview
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
Versions 3.11.1, 3.10.1 and 3.5.0 are installed on the CSF.
Note that other tools such as metaSPAdes are included in SPAdes. Run spades.py -h to see the command-line flags accepted by spades (for example --meta).
Restrictions on use
This software is open source and may be used by any CSF user. Please ensure that you cite your usage in any results or publications as per the developers documentation.
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/spades/3.11.1 module load apps/binapps/spades/3.10.1 module load apps/binapps/spades/3.5.0
Running the application
Please do not run SPAdes on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission – coming soon
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # $NSLOTS will be set automatically to 1 in a serial job spades.py --threads $NSLOTS -1 file1.in -2 file2.in -o output_dir
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission – checking if possible
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Number of cores (2--24 permitted) # $NSLOTS will be set automatically to the number of cores given above spades.py --threads $NSLOTS -1 file1.in -2 file2.in -o output_dir
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.