GapFiller-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.1.1

Author / Distributor

GapFiller

Description

"GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data." More details are at GapFiller

Running Program

The last version of this application is at /usr/local/apps/eb/GapFiller/2.1.1-foss-2016b

To use this version, please load the module with

ml GapFiller/2.1.1-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_GapFiller
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=GapFiller.%j.out

cd $SLURM_SUBMIT_DIR
ml GapFiller/2.1.1-foss-2016b
NA [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml GapFiller/2.1.1-foss-2016b 
NA NA 

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Installation

Source code is obtained from GapFiller

System

64-bit Linux