Introduction

While aiming to determine orientations and orders of fragmented contigs, scaffolding is an essential step of assembly pipelines and can make assembly results more complete. Most existing scaffolding tools adopt scaffold graph approaches. However, due to repetitive regions in genome, sequencing errors and uneven sequencing depth, constructing an accurate scaffold graph is still a challenge task.In this paper, we present a novel algorithm (called BOSS), which employs paired reads for scaffolding. To construct a scaffold graph, BOSS utilizes the distribution of insert size to decide whether an edge between two vertices (contigs) should be added and how an edge should be weighed. Moreover, BOSS adopts an iterative strategy to detect spurious edges whose removal can guarantee no contradictions in the scaffold graph. Based on the scaffold graph constructed, BOSS employs a heuristic algorithm to sort vertices (contigs) and then generates scaffolds. The experimental results demonstrate that BOSS produces more satisfactory scaffolds, compared with other popular scaffolding tools on real sequencing data of four genomes.BOSS is publicly available for download at https://github.com/bioinfomaticsCSU/BOSS CONTACT: jxwang@mail.csu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. BOSS: a novel scaffolding algorithm based on an optimized scaffold graph.
    Cite this
    Luo J, Wang J, Zhang Z, Li M, Wu FX, 2017-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Junwei Luo
    Developer

    College of Computer Science and Technology, Henan Polytechnic University, China

  2. Jianxin Wang
    Developer

    School of Information Science and Engineering, Central South University, China

  3. Zhen Zhang
    Developer

    School of Information Science and Engineering, Central South University, China

  4. Min Li
    Developer

    School of Information Science and Engineering, Central South University, China

  5. Fang-Xiang Wu
    Investigator

    Division of Biomedical Engineering, University of Saskatchewan, Canada

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Summary
AccessionBT000596
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionCanada
Submitted ByFang-Xiang Wu