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.
Versions
3.02
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
Module
You can load the modules by:
module load biocontainers
module load glimmer
Example job
Warning
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