SOAPdenovo2-Teaching: Difference between revisions
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === r240 === Au...") |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 23: | Line 23: | ||
The last version of this application is at /usr/local/apps/eb/SOAPdenovo2/r240-foss-2016b | The last version of this application is at /usr/local/apps/eb/SOAPdenovo2/r240-foss-2016b | ||
To use this version, please | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml SOAPdenovo2/r240-foss-2016b | ml SOAPdenovo2/r240-foss-2016b | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
<div class="gscript2"> | <div class="gscript2"> | ||
| Line 40: | Line 40: | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=SOAPdenovo2.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=SOAPdenovo2.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=SOAPdenovo2.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
| Line 59: | Line 60: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml SOAPdenovo2/r240-foss-2016b | ml SOAPdenovo2/r240-foss-2016b | ||
SOAPdenovo-127mer --help | |||
Version 2.04: released on July 13th, 2012 | Version 2.04: released on July 13th, 2012 | ||
Latest revision as of 13:10, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
r240
Author / Distributor
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
#SBATCH --error=SOAPdenovo2.%j.err
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 --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
Installation
Source code is obtained from SOAPdenovo2
System
64-bit Linux