MUMmer-Teaching

Category

Bioinformatics

Program On

Teaching

Version

3.23

Author / Distributor

MUMmer

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 loads the module with

ml MUMmer/3.23-foss-2016b 

Here is an example of a shell script, sub.sh, to run on at 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

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 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

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Installation

Source code is obtained from MUMmer

System

64-bit Linux