This is the Linux app named SplitMEM to run in Linux online 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 to run in Linux online
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++
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.