Difference between revisions of "MUMmer"

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m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
m (Text replacement - "#uppercase" to "uc")
 
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[[Category:Software]][[Category:Bioinformatics]]
 
[[Category:Software]][[Category:Bioinformatics]]
<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|mummer}}
 
|{{#vardefine:app|mummer}}
 
|{{#vardefine:url|http://mummer.sourceforge.net/}}
 
|{{#vardefine:url|http://mummer.sourceforge.net/}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
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|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 
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MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
 
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
 
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<!--Modules-->
==Available versions==
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==Environment Modules==
* 3.22, 3.23 on RedHat EL6 nodes
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
''Note: mummer requires the perl module to be loaded''
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==System Variables==
<!-- -->
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: mod}}|==Execution Environment and Modules==
 
 
 
To use {{#var:app}} with the environment modules system at HPC the following commands are available:
 
 
 
Get module information for {{lc: {{PAGENAME}}}}:
 
$module spider {{#var:app}}
 
{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}}
 
Load the perl module:
 
$module load perl
 
Load the application module:
 
$module load {{#var:app}}
 
or in one command:
 
$module load perl mummer
 
 
 
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
 
 
 
* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}}
 
* HPC_MUMMER_BIN - executable directory
 
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
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{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 
If you publish research that uses {{{app}}} you have to cite it as follows:
 
If you publish research that uses {{{app}}} you have to cite it as follows:
WRITE CITATION HERE
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 +
MUMmer4 pre-print:
 +
 
 +
MUMmer4: A fast and versatile genome alignment system
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Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. (2018) [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005944 MUMmer4: A fast and versatile genome alignment system.] PLOS Computational Biology 14(1): e1005944. https://doi.org/10.1371/journal.pcbi.1005944
 
|}}
 
|}}

Latest revision as of 21:21, 6 December 2019

Description

mummer website  

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

Environment Modules

Run module spider mummer to find out what environment modules are available for this application.

System Variables

  • HPC_MUMMER_DIR - installation directory




Citation

If you publish research that uses {{{app}}} you have to cite it as follows:

MUMmer4 pre-print:

MUMmer4: A fast and versatile genome alignment system Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. (2018) MUMmer4: A fast and versatile genome alignment system. PLOS Computational Biology 14(1): e1005944. https://doi.org/10.1371/journal.pcbi.1005944