SOAPdenovo2-Teaching

Category

Bioinformatics

Program On

Teaching

Version

r240

Author / Distributor

SOAPdenovo2

Description

"SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo." More details are at SOAPdenovo2

Running Program

The last version of this application is at /usr/local/apps/eb/SOAPdenovo2/r240-foss-2016b

To use this version, please load the module with

ml SOAPdenovo2/r240-foss-2016b 

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

#!/bin/bash
#SBATCH --job-name=j_SOAPdenovo2
#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=SOAPdenovo2.%j.out

cd $SLURM_SUBMIT_DIR
ml SOAPdenovo2/r240-foss-2016b
SOAPdenovo-127mer [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 SOAPdenovo2/r240-foss-2016b 
SOAPdenovo-127mer SOAPdenovo-127mer --help

Version 2.04: released on July 13th, 2012
Compile Dec  1 2017	22:19:06

Usage: SOAPdenovo <command> [option]
    pregraph        construct kmer-graph
    sparse_pregraph construct sparse kmer-graph
    contig          eliminate errors and output contigs
    map             map reads to contigs
    scaff           construct scaffolds
    all             do pregraph-contig-map-scaff in turn

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Installation

Source code is obtained from SOAPdenovo2

System

64-bit Linux