glimmer
Link to section 'Introduction' of 'glimmer' Introduction
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
For more information, please check its website: https://biocontainers.pro/tools/glimmer and its home page: http://ccb.jhu.edu/software/glimmer/index.shtml.
Link to section 'Versions' of 'glimmer' Versions
- 3.02
Link to section 'Commands' of 'glimmer' Commands
- anomaly
- build-fixed
- build-icm
- entropy-profile
- entropy-score
- extract
- g3-from-scratch.csh
- g3-from-training.csh
- g3-iterated.csh
- get-motif-counts.awk
- glim-diff.awk
- glimmer3
- long-orfs
- match-list-col.awk
- multi-extract
- not-acgt.awk
- score-fixed
- start-codon-distrib
- test
- uncovered
- upstream-coords.awk
- window-acgt
Link to section 'Module' of 'glimmer' Module
You can load the modules by:
module load biocontainers
module load glimmer
Link to section 'Example job' of 'glimmer' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Glimmer on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=glimmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers glimmer
long-orfs -n -t 1.15 scaffolds.fasta run1.longorfs
extract -t scaffolds.fasta run1.longorfs > run1.train
build-icm -r run1.icm < run1.train
glimmer3 scaffolds.fasta run1.icm cm