This is the Linux app named SplitMEM whose latest release can be downloaded as splitmem.1.0.tgz. It can be run online in the free hosting provider OnWorks for workstations.
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SplitMEM
DESCRIPTION:
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal.
Audience
Science/Research
User interface
Command-line
Programming Language
C++
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/splitmem/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.