e-mem
Efficient computation of Maximal Exact Matches for very large genomes
Command lineScience
Not tested on a device yet. What that means
Commands in the package
e-mem
About e-mem
From Debian's package description
E-MEM enables efficient computation of Maximal Exact Matches (MEMs) that does not use full text indexes. The algorithm uses much less space and is highly amenable to parallelization. It can compute all MEMs of minimum length 100 between the whole human and mouse genomes on a 12 core machine in 10 min and 2 GB of memory; the required memory can be as low as 600 MB. It can run efficiently genomes of any size. Extensive testing and comparison with currently best algorithms is provided.
Mummer has many different scripts where one of the key program is MEM computation. In all the scripts, the MEM computation program can be replaced with e-mem with ease for better performance.
From Debian's description of the e-mem package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libgomp1libstdc++6
Related apps
- toulbar2Exact combinatorial optimization for Graphical ModelsCommand line
- qsopt-exExact linear programming solverCommand line
- kraken2taxonomic classification system using exact k-mer matchesCommand line
- sumatrafast and exact comparison and clustering of sequencesCommand line
- murasakihomology detection tool across multiple large genomesCommand line
- fastaniFast alignment-free computation of whole-genome Average Nucleotide IdentityCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the e-mem package, under that package's license.
- Description: Debian's description of the e-mem package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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