View source for MUMmer

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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
{|<!--Main settings - REQUIRED-->
|{{#vardefine:app|mummer}}
|{{#vardefine:url|http://mummer.sourceforge.net/}}
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
|}
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
{{#if: {{#var: citation}}|==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) [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
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