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2017 | OriginalPaper | Chapter

On the Linearization of Scaffolds Sharing Repeated Contigs

Authors : Mathias Weller, Annie Chateau, Rodolphe Giroudeau

Published in: Combinatorial Optimization and Applications

Publisher: Springer International Publishing

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Abstract

Scaffolding is the final step in assembling Next Generation Sequencing data, in which pre-assembled contiguous regions (“contigs”) are oriented and ordered using information that links them (for example, mapping of paired-end reads). As the genome of some species is highly repetitive, we allow placing some contigs multiple times, thereby generalizing established computational models for this problem. We study the subsequent problems induced by the translation of solutions of the model back to actual sequences, proposing models and analyzing the complexity of the resulting computational problems. We find both polynomial-time and \(\mathcal {NP}\)-hard special cases like planarity or bounded degree.

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previous chapter Planar Vertex-Disjoint Cycle Packing: New Structures and Improved Kernel
next chapter A Memetic Algorithm for the Linear Ordering Problem with Cumulative Costs
Footnotes
1
Solution graphs differ from scaffold graphs in that they might not abide by the condition that m(uv) equals the smaller of the multiplicities of the contig edges incident with u and v.
 
2
The “Exponential Time Hypothesis” (ETH) states that boolean satisfiability (SAT) cannot be decided in \(2^{o(n)}\) time, where n is the number of variables in the formula.
 
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Metadata
Title
On the Linearization of Scaffolds Sharing Repeated Contigs
Authors
Mathias Weller
Annie Chateau
Rodolphe Giroudeau
Copyright Year
2017
Book
Combinatorial Optimization and Applications

Print ISBN: 978-3-319-71146-1

Electronic ISBN: 978-3-319-71147-8

Copyright Year: 2017

DOI
https://doi.org/10.1007/978-3-319-71147-8_38

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