SPAdes
Description
SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. It is intended for both standard (multicell) and single-cell MDA bacteria assemblies.
Licence
GPL version 2.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of spades and load default version of spades as
module avail spades/ # list available modules module load spades # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail spades
and choose explicit version you want to use. Then run as
rnaspades.py --help rnaspades.py
In the qsub command is necessary to specify parameter ompthreads to allow run on multiple threads, e.g. (for 8 threads run)
qsub -l select=1:ncpus=8:ompthreads=8:mem=...
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SPAdes is not able to utilize more than 6 CPUs on average. Reservation of more than 8 CPUs will not be beneficial for the speedup of calculation.
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