A complexity and approximation framework for the maximization scaffolding problem

Château, Annie; Giroudeau, Rodolphe

doi:10.1016/j.tcs.2015.06.023

Cited by 20 publications

(37 citation statements)

References 23 publications

(33 reference statements)

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“…Furthermore, by the condition (iii), SAG(M) consists entirely of alternating paths. A similar optimization problem, where the number of paths and the number cycles in the resulting SAG(M) are fixed, is known to be NPcomplete [31], leaving a little hope for the RMMP to have a polynomial-time solution. Instead, CAMSA employs two merging heuristic solutions building upon the previously proposed algorithms [31,32] as described below in this section.…”

Section: Problem 2 (Restricted Maximum Matching Problem Rmmp) Given mentioning

confidence: 99%

CAMSA: A tool for comparative analysis and merging of scaffold assemblies

Aganezov

Alekseyev

2016

2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

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Background: Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose positions and orientations along the genome are unknown. While there exists a number of methods for reconstruction of the genome from its scaffolds, utilizing various computational and wet-lab techniques, they often can produce only partial error-prone scaffold assemblies. It therefore becomes important to compare and merge scaffold assemblies produced by different methods, thus combining their advantages and highlighting present conflicts for further investigation. These tasks may be labor intensive if performed manually. Results: We present CAMSA-a tool for comparative analysis and merging of two or more given scaffold assemblies. The tool (i) creates an extensive report with several comparative quality metrics; (ii) constructs the most confident merged scaffold assembly; and (iii) provides an interactive framework for a visual comparative analysis of the given assemblies. Among the CAMSA features, only scaffold merging can be evaluated in comparison to existing methods. Namely, it resembles the functionality of assembly reconciliation tools, although their primary targets are somewhat different. Our evaluations show that CAMSA produces merged assemblies of comparable or better quality than existing assembly reconciliation tools while being the fastest in terms of the total running time. Conclusions: CAMSA addresses the current deficiency of tools for automated comparison and analysis of multiple assemblies of the same set scaffolds. Since there exist numerous methods and techniques for scaffold assembly, identifying similarities and dissimilarities across assemblies produced by different methods is beneficial both for the developers of scaffold assembly algorithms and for the researchers focused on improving draft assemblies of specific organisms.

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Section: Problem 2 (Restricted Maximum Matching Problem Rmmp) Given mentioning

confidence: 99%

CAMSA: A tool for comparative analysis and merging of scaffold assemblies

Aganezov

Alekseyev

2016

2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

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“…Furthermore, by the condition (iii), SAG(M ) consists entirely of alternating paths. A similar optimization problem, where the number of paths and the number cycles in the resulting SAG(M ) are fixed, is known to be NP-complete [10], leaving a little hope for the RMMP to have a polynomial-time solution. Instead, CAMSA employs two merging heuristic solutions building upon the previously proposed algorithms [31,10] as described below in this section.…”

Section: Merging Assembliesmentioning

confidence: 99%

CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies

Aganezov

Alekseyev

2016

Preprint

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Motivation: Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose positions and orientations along the genome are unknown. While there exists a number of methods for reconstruction of the genome from its scaffolds, utilizing various computational and wet-lab techniques, they often can produce only partial error-prone scaffold assemblies. It therefore becomes important to compare and merge scaffold assemblies produced by different methods, thus combining their advantages and highlighting present conflicts for further investigation. These tasks may be labor intensive if performed manually.Results: We present CAMSA-a tool for comparative analysis and merging of two or more given scaffold assemblies. The tool (i) creates an extensive report with several comparative quality metrics; (ii) constructs the most confident merged scaffold assembly; and (iii) provides an interactive framework for a visual comparative analysis of the given assemblies. Among the CAMSA features, only scaffold merging can be evaluated in comparison to existing methods. Namely, it resembles the functionality of assembly reconciliation tools, although their primary targets are somewhat different. Our evaluations show that CAMSA produces merged assemblies of comparable or better quality than existing assembly reconciliation tools while being the fastest in terms of the total running time.Availability: CAMSA is distributed under the MIT license and is available at http://cblab. org/camsa/.

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“…The scaffolding operation then aims at selecting the best paths in this graph in order to produce longer genomic sequences called scaffolds. Previous work focuses on the production of sequences by solving the so-called Scaffolding problem in this graph [4,14,16]. Scaffolding is a widely studied problem in bioinformatics and can be modeled by numerous, mostly heuristic, methods [8].…”

Section: Introductionmentioning

confidence: 99%

Linearizing Genomes: Exact Methods and Local Search

Davot

Château

Giroudeau

et al. 2020

SOFSEM 2020: Theory and Practice of Computer Science

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In this article, we address the problem of genome linearization from the perspective of Polynomial Local Search, a complexity class related to finding local optima. We prove that the linearization problem, with a neighborhood structure, the neighbor slide, is PLS-complete. On the positive side, we develop two exact methods, one using tree decompositions with an efficient dynamic programming, the other using an integer linear programming. Finally, we compare them on real instances. a b c d e f g h AT CT T m = 1 CCT m = 2 T AA m = 1 CAT G m = 1 26 7 9 3 1 1 2

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A complexity and approximation framework for the maximization scaffolding problem

Cited by 20 publications

References 23 publications

CAMSA: A tool for comparative analysis and merging of scaffold assemblies

CAMSA: A tool for comparative analysis and merging of scaffold assemblies

CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies

Linearizing Genomes: Exact Methods and Local Search

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