On the Linearization of Scaffolds Sharing Repeated Contigs

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 placi...

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Bibliographic Details
Published inCombinatorial Optimization and Applications Vol. 10628; pp. 509 - 517
Main Authors Weller, Mathias, Chateau, Annie, Giroudeau, Rodolphe
Format Book Chapter
LanguageEnglish
Published Switzerland Springer International Publishing AG 2017
Springer International Publishing
SeriesLecture Notes in Computer Science
Online AccessGet full text
ISBN9783319711461
3319711466
ISSN0302-9743
1611-3349
DOI10.1007/978-3-319-71147-8_38

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Summary: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 NP $$\mathcal {NP}$$ -hard special cases like planarity or bounded degree.
Bibliography:Original 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 NP\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathcal {NP}$$\end{document}-hard special cases like planarity or bounded degree.
ISBN:9783319711461
3319711466
ISSN:0302-9743
1611-3349
DOI:10.1007/978-3-319-71147-8_38