MUMmer¶

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.

Environment Variables¶

HPC_MUMMER_DIR - installation directory
HPC_MUMMER_BIN - executable directory
HPC_MUMMER_LIB - library directory
HPC_MUMMER_INC - include directory

Citation¶

If you publish research that uses MUMmer you have to cite it as follows:

Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. PLOS Computational Biology, 14(1), e1005944. https://doi.org/10.1371/journal.pcbi.1005944

Categories¶

biology, genomics