plasme¶

Description¶

PLASMe is a tool to identify plasmid contigs from short-read assemblies using the Transformer. PLASMe capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe, while diverged plasmids can be predicted using order-specific Transformer models.

DB - database directory

Environment Modules¶

Run module spider plasme to find out what environment modules are available for this application.

Environment Variables¶

HPC_PLASME_DIR - installation directory
HPC_PLASME_BIN - executable directory

Additional Usage Information¶

The database path defaults to the user's working directory, and there is no way to specify the DB path in the command line options. Therefore, to use the database provided by the developers you need to create a symbolic link to it in your PWD. I've set the database path in the env variable $DB, so the command ln -s $DB DB will set the DB correctly for use.

Install was successfully tested with provided test data with the following commands:

$ ml plasme/1.1

$ ln -s $DB DB

$ PLASMe.py test.fasta test.plasme.fna -c 0.6 -i 0.6 -p 0.5 -t 8

Categories¶

Genomics