SPAdes

module avail spades/

SPAdes is an assembly toolkit containing various assembly pipelines. It is intended for both standard (multicell) and single-cell MDA bacteria assemblies.

Usage

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=...

Tip

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.