A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome
2024
Edward Spinard | Mark Dinhobl | Cassidy N. G. Erdelyan | James O’Dwyer | Jacob Fenster | Hillary Birtley | Nicolas Tesler | Sten Calvelage | Mikael Leijon | Lucilla Steinaa | Vivian O’Donnell | Sandra Blome | Armanda Bastos | Elizabeth Ramirez-Medina | Anna Lacasta | Karl Ståhl | Huaji Qiu | Dachrit Nilubol | Chandana Tennakoon | Charles Maesembe | Bonto Faburay | Aruna Ambagala | David Williams | Paolo Ribeca | Manuel V. Borca | Douglas P. Gladue
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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