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SplitMEM: Graphical pan-genome analysis with suffix skips

Shoshana Marcus, Hayan Lee, Michael C. Schatz
doi: https://doi.org/10.1101/003954
Shoshana Marcus
1Simons Center for Quantitive Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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Hayan Lee
1Simons Center for Quantitive Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
2Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794, USA
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Michael C. Schatz
1Simons Center for Quantitive Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
2Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794, USA
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ABSTRACT

Motivation 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. One of the most sophisticated data structures for representing an entire population of genomes is a compressed de Bruijn graph. The graph structure can robustly represent simple SNPs to complex structural variations far beyond what can be done from linear sequences alone. As such there is a strong need to develop algorithms that can efficiently construct and analyze these graphs.

Results In this paper we explore the deep topological relationships between the suffix tree and the compressed de Bruijn graph. 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) into the graph nodes. We demonstrate the utility of splitMEM by analyzing the pan-genomes of 9 strains of Bacillus anthracis and 9 strains of Escherichia coli to reveal the properties of their core genomes.

Availability The source code and documentation are available open-source at http://splitmem.sourceforge.net

Contact mschatz{at}cshl.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 06, 2014.
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SplitMEM: Graphical pan-genome analysis with suffix skips
Shoshana Marcus, Hayan Lee, Michael C. Schatz
bioRxiv 003954; doi: https://doi.org/10.1101/003954
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SplitMEM: Graphical pan-genome analysis with suffix skips
Shoshana Marcus, Hayan Lee, Michael C. Schatz
bioRxiv 003954; doi: https://doi.org/10.1101/003954

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