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coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies

View ORCID ProfileDmitry Meleshko, Iman Hajirasouliha, View ORCID ProfileAnton Korobeynikov
doi: https://doi.org/10.1101/2020.07.28.224584
Dmitry Meleshko
1Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, 10021, New York, USA
2Center for Algorithmic Biotechnology, St. Petersburg State University, 199004, St. Peterburg, Russia
3Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, NY, 10021, USA
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  • ORCID record for Dmitry Meleshko
Iman Hajirasouliha
3Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, NY, 10021, USA
4Englander Institute for Precision Medicine, The Meyer Cancer Center, Weill Cornell Medicine, NY, 10021, USA
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Anton Korobeynikov
2Center for Algorithmic Biotechnology, St. Petersburg State University, 199004, St. Peterburg, Russia
5Department of Statistical Modelling, St. Petersburg State University, 198504, St. Peterburg, Russia
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  • ORCID record for Anton Korobeynikov
  • For correspondence: a.korobeynikov@spbu.ru
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ABSTRACT

The COVID-19 pandemic has ignited a broad scientific interest in coronavirus research. The identification of coronaviral species in natural reservoirs typically involves de novo assembly. However, existing genome, metagenome and transcriptome assemblers often are not able to assemble coronaviruses into a single contig. Coverage variation between datasets and within dataset, presence of close strains, and contamination set a high bar for assemblers to process datasets with diverse properties. We developed coronaSPAdes, a new module of the SPAdes assembler for RNA viral species recovery in general and coronaviruses in particular. coronaSPAdes leverages the knowledge about viral genome structures to improve assembly. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read and viral assemblers in the recovery of full-length RNA viral genomes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Added RNA viral assemblies (HIV, Influenza)

  • http://cab.spbu.ru/software/coronaspades/

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 February 01, 2021.
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coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
Dmitry Meleshko, Iman Hajirasouliha, Anton Korobeynikov
bioRxiv 2020.07.28.224584; doi: https://doi.org/10.1101/2020.07.28.224584
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coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
Dmitry Meleshko, Iman Hajirasouliha, Anton Korobeynikov
bioRxiv 2020.07.28.224584; doi: https://doi.org/10.1101/2020.07.28.224584

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