The St. Petersburg Academic Univesrity genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies.
Sample scripts for SPAdes use are available in directory /opt/packages/examples/spades on Bridges.
Usage on Bridges-2
To see what versions of SPAdes are available and if there is more than one, which is the default, along with some help, type
module spider spades
To use SPAdes, include a command like this in your batch script or interactive session to load the SPAdes module: (note ‘module load’ is case-sensitive):
module load SPAdes
Usage on Bridges
To see what versions of SPAdes are available type
module avail spades
To see what other modules are needed, what commands are available and how to get additional help type
module help spades
To use SPAdes, include a command like this in your batch script or interactive session to load the SPAdes module:
module load spades
Be sure you also load any other modules needed, as listed by the
module help spades command.