SPAdes 3.10.1

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

Accessing the software

To load the module:

$ module load apps/spades/3.10.1

An example command to include in your job script:

$ spades.py <options> -o <output_dir>

Example: SPAdes Job

An example can be found at ${BB_EXAMPLES}/SPAdes/sbatch.sh. The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/SPAdes ~/spades-test
$ cd ~/spades-test

Edit the sbatch.sh script according to your needs, then do:

$ sbatch sbatch.sh

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Read the manual for more information about this version of the application.

 


Last modified: 19 July 2017