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[ Source: e-mem  ]

Package: e-mem (1.0.1-4)

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Efficient computation of Maximal Exact Matches for very large genomes

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.

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Download for all available architectures
Architecture Package Size Installed Size Files
amd64 34.1 kB106.0 kB [list of files]
arm64 30.9 kB94.0 kB [list of files]
armel 33.9 kB101.0 kB [list of files]
armhf 33.5 kB81.0 kB [list of files]
i386 40.2 kB117.0 kB [list of files]
mips64el 33.6 kB117.0 kB [list of files]
mipsel 40.9 kB120.0 kB [list of files]
ppc64el 34.4 kB162.0 kB [list of files]
s390x 31.5 kB102.0 kB [list of files]