SplitMEM

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.

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License

Apache License V2.0

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Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

C++

Related Categories

C++ Bio-Informatics Software

Registered

2014-04-04

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