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. | ||
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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 | |
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{{#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: | ||
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| + | MUMmer4 pre-print: | ||
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| + | 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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Revision as of 21:21, 6 December 2019
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