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SCIENCE CHINA Life Sciences, Volume 63 , Issue 1 : 160-164(2020) https://doi.org/10.1007/s11427-019-9828-1

Nanopore sequencing of African swine fever virus

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  • ReceivedAug 25, 2019
  • AcceptedSep 16, 2019
  • PublishedNov 5, 2019

Abstract

There is no abstract available for this article.


Funded by

the National Key R&D Program of China(2016YFC1200800,&,2018YFC0840402)

Research Project of African Swine Fever of Chinese Academy of Sciences(KJZD-SW-L06)

China Mega-Project for Infectious Disease(2017ZX10103005-005)

the State Key Laboratory of Veterinary Biotechnology Research Fund(SKLVBF201902)


Acknowledgment

This work was supported by the National Key R&D Program of China (2016YFC1200800 & 2018YFC0840402), Research Project of African Swine Fever of Chinese Academy of Sciences (KJZD-SW-L06), China Mega-Project for Infectious Disease (2017ZX10103005-005), the State Key Laboratory of Veterinary Biotechnology Research Fund (SKLVBF201902). J.L. is supported by Youth Innovation Promotion Association of CAS (2019091). We acknowledge Lei Zhang (the Core Facility and Technical Support in the Wuhan Institute of Virology, CAS) for supporting in the genome sequencing.


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Figure S1 Maximum likelihood phylogenetic tree of p72 gene sequences.

Figure S2 The next-generation sequencing data was classified using centrifuge, and the proportion of ASFV and other species is shown.

Figure S3 Three sequencing approaches to obtain ASFV genome.

Table S1 Sequencing metrics

Table S2 Genome comparison

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


References

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  • Figure 1

    Nanopore sequencing of CAS19-01. The data generated by nanopore sequencing were evaluated and counted. A, The proportion of ASFV and other species in the reads. The classification results were generated by Centrifuge. B, Statistics of the length distribution of ASFV reads show that although short reads inevitably accounted for the majority, many long-length ASFV reads were obtained. C, Comparison of the genome-wide coverage and sequencing depth of the next and third generation sequencing (gray and fuchsia, respectively). Among them, the next-generation sequencing has some sites with too high sequencing depth, which are showed by gray dots. The middle track represents the variations in genome obtained by nanopore with reference to the genome obtained by NGS. The genomic information is derived from the annotated CAS19-01-NGS, and the orange-red arrow and the blue arrow represent the ORFs encoded by the positive and negative strands, respectively. D, The sequencing error rate of the raw reads of nanopore. E, Genome comparison of genotype II strains.

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