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Comparison of long read methods for sequencing and assembly of a plant genome

View ORCID ProfileValentine Murigneux, View ORCID ProfileSubash Kumar Rai, View ORCID ProfileAgnelo Furtado, View ORCID ProfileTimothy J.C. Bruxner, Wei Tian, Qianyu Ye, Hanmin Wei, Bicheng Yang, View ORCID ProfileIvon Harliwong, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, View ORCID ProfileBrock A. Peters, View ORCID ProfileMengyang Xu, Pei Wu, View ORCID ProfileBruce Topp, View ORCID ProfileLachlan J.M. Coin, View ORCID ProfileRobert J. Henry
doi: https://doi.org/10.1101/2020.03.16.992933
Valentine Murigneux
1Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072 Brisbane, Australia
3Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, Australia
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  • ORCID record for Valentine Murigneux
  • For correspondence: v.murigneux@uq.edu.au
Subash Kumar Rai
1Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072 Brisbane, Australia
3Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, Australia
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Agnelo Furtado
2Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
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  • ORCID record for Agnelo Furtado
Timothy J.C. Bruxner
3Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, Australia
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Wei Tian
4BGI-Shenzhen, Shenzhen 518083, China
5BGI-Australia, 300 Herston Road, Herston QLD 4006, Australia
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Qianyu Ye
4BGI-Shenzhen, Shenzhen 518083, China
5BGI-Australia, 300 Herston Road, Herston QLD 4006, Australia
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Hanmin Wei
4BGI-Shenzhen, Shenzhen 518083, China
6MGI, BGI-Shenzhen, Shenzhen 518083, China
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Bicheng Yang
4BGI-Shenzhen, Shenzhen 518083, China
5BGI-Australia, 300 Herston Road, Herston QLD 4006, Australia
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Ivon Harliwong
4BGI-Shenzhen, Shenzhen 518083, China
5BGI-Australia, 300 Herston Road, Herston QLD 4006, Australia
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Ellis Anderson
6MGI, BGI-Shenzhen, Shenzhen 518083, China
7Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, California 95134, USA
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Qing Mao
6MGI, BGI-Shenzhen, Shenzhen 518083, China
7Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, California 95134, USA
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Radoje Drmanac
4BGI-Shenzhen, Shenzhen 518083, China
6MGI, BGI-Shenzhen, Shenzhen 518083, China
7Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, California 95134, USA
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Ou Wang
4BGI-Shenzhen, Shenzhen 518083, China
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Brock A. Peters
4BGI-Shenzhen, Shenzhen 518083, China
6MGI, BGI-Shenzhen, Shenzhen 518083, China
7Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, California 95134, USA
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Mengyang Xu
4BGI-Shenzhen, Shenzhen 518083, China
8BGI-Qingdao, Qingdao, 266555, China
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Pei Wu
4BGI-Shenzhen, Shenzhen 518083, China
9BGI-Tianjin, Tianjin, China
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Bruce Topp
2Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
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Lachlan J.M. Coin
1Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072 Brisbane, Australia
3Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, Australia
10The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia
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Robert J. Henry
2Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
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  • ORCID record for Robert J. Henry
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Abstract

Sequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample. Here, we report a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements. Overall, the three long read technologies produced highly contiguous and complete genome assemblies of Macadamia jansenii. At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

  • List of abbreviations

    AUD
    Australian dollars
    bp
    base pairs
    BGI
    Beijing Genomics Institute
    BUSCO
    Benchmarking Universal Single-Copy Orthologs
    BWA
    Burrows-Wheeler Aligner
    g
    gram
    Gb
    gigabase pairs
    kb
    kilobase pairs
    Mb
    megabase pairs
    mg
    milligram
    μl
    microlitre
    ml
    millilitre
    mm
    millimeter
    ng
    nanogram
    ONT
    Oxford Nanopore Technologies
    PacBio
    Pacific Biosciences
    QUAST
    QUality ASsessment Tool
    SMRT
    single-molecule real-time
    SPAdes
    St. Petersburg genome assembler
    stLFR
    Single Tube Long Fragment Reads
    TB
    Terabyte
    USD
    United States Dollar
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted March 18, 2020.
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    Comparison of long read methods for sequencing and assembly of a plant genome
    Valentine Murigneux, Subash Kumar Rai, Agnelo Furtado, Timothy J.C. Bruxner, Wei Tian, Qianyu Ye, Hanmin Wei, Bicheng Yang, Ivon Harliwong, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A. Peters, Mengyang Xu, Pei Wu, Bruce Topp, Lachlan J.M. Coin, Robert J. Henry
    bioRxiv 2020.03.16.992933; doi: https://doi.org/10.1101/2020.03.16.992933
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    Comparison of long read methods for sequencing and assembly of a plant genome
    Valentine Murigneux, Subash Kumar Rai, Agnelo Furtado, Timothy J.C. Bruxner, Wei Tian, Qianyu Ye, Hanmin Wei, Bicheng Yang, Ivon Harliwong, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A. Peters, Mengyang Xu, Pei Wu, Bruce Topp, Lachlan J.M. Coin, Robert J. Henry
    bioRxiv 2020.03.16.992933; doi: https://doi.org/10.1101/2020.03.16.992933

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