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PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach

Published: 22 September 2013 Publication History

Abstract

Since the read lengths of high throughput sequencing (HTS) technologies are short, de novo assembly which plays significant roles in many applications remains a great challenge. Most of the state-of-the-art approaches base on de Bruijn graph strategy and overlap-layout strategy. However, these approaches which depend on k-mers or read overlaps do not fully utilize information of single-end and paired-end reads when resolving branches, e.g. the number and positions of reads supporting each possible extension are not taken into account when resolving branches.
We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and different read overlap size thresholds ranging from Omax to Omin to resolve the gaps and branches. Moreover, by constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. When the correct extension cannot be determined, PERGA will try to extend the contigs by all feasible extensions and determine the correct extension by using look ahead technology.
We evaluated PERGA on both simulated Illumina data sets and real data sets, and it constructed longer and more correct contigs and scaffolds than other state-of-the-art assemblers IDBA-UD, Velvet, ABySS, SGA and CABOG.
Availability: https://github.com/hitbio/PERGA

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Cited By

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  • (2022)Overview of structural variation callingComputers in Biology and Medicine10.1016/j.compbiomed.2022.105534145:COnline publication date: 23-May-2022
  • (2022)Genome sequence assembly algorithms and misassembly identification methodsMolecular Biology Reports10.1007/s11033-022-07919-849:11(11133-11148)Online publication date: 23-Sep-2022
  • (2015)misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end readsBMC Bioinformatics10.1186/s12859-015-0818-316:1Online publication date: 16-Nov-2015

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  1. PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach

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    cover image ACM Conferences
    BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
    September 2013
    987 pages
    ISBN:9781450324342
    DOI:10.1145/2506583
    Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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    Publication History

    Published: 22 September 2013

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    Author Tags

    1. Genome assembly
    2. Greedy-like prediction
    3. Look ahead technology
    4. Variable overlap sizes

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    September 22 - 25, 2013
    Wshington DC, USA

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    Overall Acceptance Rate 254 of 885 submissions, 29%

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    View all
    • (2022)Overview of structural variation callingComputers in Biology and Medicine10.1016/j.compbiomed.2022.105534145:COnline publication date: 23-May-2022
    • (2022)Genome sequence assembly algorithms and misassembly identification methodsMolecular Biology Reports10.1007/s11033-022-07919-849:11(11133-11148)Online publication date: 23-Sep-2022
    • (2015)misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end readsBMC Bioinformatics10.1186/s12859-015-0818-316:1Online publication date: 16-Nov-2015

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