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