MUMmer-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=MUMmer.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=MUMmer.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=MUMmer.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml MUMmer/3.23-foss-2016b | ml MUMmer/3.23-foss-2016b | ||
mummer -help | |||
Usage: mummer [options] <reference-file> <query-files> | Usage: mummer [options] <reference-file> <query-files> | ||
Latest revision as of 14:09, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
3.23
Author / Distributor
Description
"MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it." More details are at MUMmer
Running Program
The last version of this application is at /usr/local/apps/eb/MUMmer/3.23-foss-2016b
To use this version, please load the module with
ml MUMmer/3.23-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_MUMmer
#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=MUMmer.%j.out
#SBATCH --error=MUMmer.%j.err
cd $SLURM_SUBMIT_DIR
ml MUMmer/3.23-foss-2016b
mummer [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 MUMmer/3.23-foss-2016b mummer -help Usage: mummer [options] <reference-file> <query-files> Find and output (to stdout) the positions and length of all sufficiently long maximal matches of a substring in <query-file> and <reference-file> Options: -mum compute maximal matches that are unique in both sequences -mumcand same as -mumreference -mumreference compute maximal matches that are unique in the reference- sequence but not necessarily in the query-sequence (default) -maxmatch compute all maximal matches regardless of their uniqueness -n match only the characters a, c, g, or t they can be in upper or in lower case -l set the minimum length of a match if not set, the default value is 20 -b compute forward and reverse complement matches -r only compute reverse complement matches -s show the matching substrings -c report the query-position of a reverse complement match relative to the original query sequence -F force 4 column output format regardless of the number of reference sequence inputs -L show the length of the query sequences on the header line -h show possible options -help show possible options
Installation
Source code is obtained from MUMmer
System
64-bit Linux