Difference between revisions of "MUMmer"

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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-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Execution Environment and Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
To use {{#var:app}} with the environment modules system at HPC the following commands are available:
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==System Variables==
 
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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: 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:
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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
 
|}}
 
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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