A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome

Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations. We developed an automated, standardized pipeline for the analysis of NGS reads that directly provides users with assemblies and annotations formatted for their submission to NCBI. This pipeline is freely available on GitHub and has been tested through the GARA partners by examining two previously sequenced ASFV genomes; this study also aimed to assess the accuracy and limitations of two strategies present within the pipeline: reference-based (Illumina reads) and de novo assembly (Illumina and Nanopore reads) strategies.

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Publication Details

Journal
Viruses
Published
2024-08-13
DOI
https://doi.org/10.3390/v16081293
Citations
7
Primary Topic
Animal Disease Management and Epidemiology
Type
article
Field-Weighted Citation Impact
3.97

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A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome

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A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome

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article en
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Abstract

Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations. We developed an automated, standardized pipeline for the analysis of NGS reads that directly provides users with assemblies and annotations formatted for their submission to NCBI. This pipeline is freely available on GitHub and has been tested through the GARA partners by examining two previously sequenced ASFV genomes; this study also aimed to assess the accuracy and limitations of two strategies present within the pipeline: reference-based (Illumina reads) and de novo assembly (Illumina and Nanopore reads) strategies.

VirusesVol. 16(8)
Oak Ridge Associated Universities (US), The Pirbright Institute (GB), Commonwealth Scientific and Industrial Research Organisation (AU), Canadian Food Inspection Agency (CA), Friedrich-Loeffler-Institut (DE), Agricultural Research Service (US), United States Department of Agriculture (US), Australian Centre for Disease Preparedness (AU), Chulalongkorn University (TH), Onderstepoort Veterinary Academic Hospital (ZA), Plum Island Animal Disease Center (US), Biomathematics and Statistics Scotland (GB), Chinese Academy of Agricultural Sciences (CN), UK Health Security Agency (GB), Oak Ridge Institute for Science and Education, International Livestock Research Institute (KE), University of Pretoria (ZA), Harbin Veterinary Research Institute (CN), Makerere University (UG)
U.S. Department of Energy, U.S. Department of Agriculture, Oak Ridge Associated Universities, Oak Ridge Institute for Science and Education
Openalex Percentile: Top 7%
Animal Disease Management and Epidemiology
3.97
DOIOpen Access PDFOpenAlex
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