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Parameter exploration improves the accuracy of long-read genome assembly

View ORCID ProfileAnurag Priyam, View ORCID ProfileAlicja Witwicka, View ORCID ProfileAnindita Brahma, View ORCID ProfileEckart Stolle, View ORCID ProfileYannick Wurm
doi: https://doi.org/10.1101/2021.05.28.446135
Anurag Priyam
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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  • ORCID record for Anurag Priyam
  • For correspondence: anurag.priyam@qmul.ac.uk y.wurm@qmul.ac.uk
Alicja Witwicka
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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  • ORCID record for Alicja Witwicka
Anindita Brahma
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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  • ORCID record for Anindita Brahma
Eckart Stolle
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
2Leibniz Institute of Animal Biodiversity, Zoological Research Museum Alexander Koenig, Bonn, Germany
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Yannick Wurm
1School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
3Alan Turing Institute, London, UK
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  • For correspondence: anurag.priyam@qmul.ac.uk y.wurm@qmul.ac.uk
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Abstract

Long-molecule sequencing is now routinely applied to generate high-quality reference genome assemblies. However, datasets differ in repeat composition, heterozygosity, read lengths and error profiles. The assembly parameters that provide the best results could thus differ across datasets. By integrating four complementary and biologically meaningful metrics, we show that simple fine-tuning of assembly parameters can substantially improve the quality of long-read genome assemblies. In particular, modifying estimates of sequencing error rates improves some metrics more than two-fold. We provide a flexible software, CompareGenomeQualities, that automates comparisons of assembly qualities for researchers wanting a straightforward mechanism for choosing among multiple assemblies.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email addresses of all authors: anurag.priyam{at}qmul.ac.uk, a.witwicka{at}qmul.ac.uk, a.brahma{at}qmul.ac.uk, e.stolle{at}leibniz-zfmk.de, y.wurm{at}qmul.ac.uk

  • https://github.com/wurmlab/CompareGenomeQualities

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 May 30, 2021.
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Parameter exploration improves the accuracy of long-read genome assembly
Anurag Priyam, Alicja Witwicka, Anindita Brahma, Eckart Stolle, Yannick Wurm
bioRxiv 2021.05.28.446135; doi: https://doi.org/10.1101/2021.05.28.446135
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Parameter exploration improves the accuracy of long-read genome assembly
Anurag Priyam, Alicja Witwicka, Anindita Brahma, Eckart Stolle, Yannick Wurm
bioRxiv 2021.05.28.446135; doi: https://doi.org/10.1101/2021.05.28.446135

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