Glimmer is a set of bioinformatics programs designed primarily for use with microbial genomic data sets. It is designed to find genes and separate out coding regions from non-coding regions in these datasets using an Interpolated Markov Model approach.
Using Glimmer on RCC Resources
Running Glimmer Sequentially on RCC Systems
Glimmer's program set requires the gnu module to be loaded in order to use it on HPC. There are numerous commands available within Glimmer. For a complete list and usage documentation, please refer to the main website as there are release notes available there for this purpose. In order to run a command like
glimmer3 on HPC, simply run the command:
module load gnu glimmer3 -[OPTIONS] SEQ_FILE ICM_FILE OUTPUT
In the example above, there are a long list of options available with glimmer3. The SEQ_FILE argument should be a genetic sequence file and the ICM_FILE is an Interpolated Context Model file which is required for Glimmer's program. If you do not have a pre-made ICM file, one can be generated from training sequences using the
build-icm command. Note that the build-icm command may require you to specify the entire path to the build-icm executable which is
/opt/rcc/gnu/libexec/glimmer3/build-icm [OPTS] FILE. Detailed usage documentation on this and all other component programs can be found in the release notes on the main website. There are also various output options that would go in OUTPUT. You can request a .detail file or a .predict file for details and model predictions respectively.