Revision as of 10:49, 16 November 2022

Application Details

• Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases.
• Version: 2.31.8
• Modules: maker/2.31.8
• Licence: GNU General Public License developed by the Free Software Foundation.

Usage

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its outputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.

Maker depends on the following modules on Viper

• module add ncbi-blast/2.4.0
• module add perl/5.24.0

These are loaded automatically with

• module add maker/2.31.8

Non Interactive

Note: this example is done on a high memory node, usually access would be achieved with the scheduler

[username@c230 ~]$ module add maker/2.31.8
[username@c230 ~]$ maker --ignore_nfs_tmp

Interactive

Through SLURM this would become the script:

A typical script would be:

#!/bin/bash
#SBATCH -J maker
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o out
#SBATCH -e err
#SBATCH -p highmem
#SBATCH --exclusive

module purge
module add gcc/4.9.3
module add maker/2.31.8

maker --ignore_nfs_tmp

This is then submitted as follows:

[username@login01 ~]$ sbatch makerDEMO.job
Submitted batch job 289522

Next Steps

• http://www.yandell-lab.org/software/maker.html

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