MUMmer: Difference between revisions
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Moskalenko (talk | contribs) m Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} " |
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__NOTOC__ | __NOTOC__ | ||
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[[Category:Software]][[Category: | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | ||
{|<!--Main settings - REQUIRED--> | |||
{| | |||
<!--Main settings - REQUIRED--> | |||
|{{#vardefine:app|mummer}} | |{{#vardefine:app|mummer}} | ||
|{{#vardefine:url|http://mummer.sourceforge.net/}} | |{{#vardefine:url|http://mummer.sourceforge.net/}} | ||
|{{#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 --> | |{{#vardefine:citation|1}} <!--Enable Reference/Citation section --> | ||
|} | |} | ||
<!-- ######## Template Body ######## --> | <!-- ######## Template Body ######## --> | ||
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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. | ||
<!-- | <!--Modules--> | ||
==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 | |||
< | |||
* HPC_{{uc:{{#var:app}}}}_DIR - | |||
{{#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 | {{#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: | ||
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 | |||
|}} | |}} | ||
Latest revision as of 13:39, 19 August 2022
Description
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