ArticleViruses2024
A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome.
Article in Viruses, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Oral administration ofApplied and environmental microbiology · 2026Article
- Characterization of African swine fever outbreaks in Hong Kong SAR, winter 2023 to 2024.Microbiology spectrum · 2026Article
- 'PePApipe': A complete bioinformatics analysis pipeline for African Swine Fever Virus genome.PloS one · 2026Article
- Advances and emerging technologies in the diagnosis of viral infections in pigs: Progress, challenges, and One Health perspectives.Veterinary world · 2025Review
- The First CRISPR-Based Therapeutic (SL_1.52) for African Swine Fever Is Effective in Swine.Viruses · 2025Article
- Complete African swine fever virus genome isolated from the 2023 outbreak in Cameroon.Microbiology resource announcements · 2025Article
- Propagation and Sequencing of African Swine Fever Virus on Porcine-Derived Buffy Coat Fraction Cells.Transboundary and emerging diseases · 2025Article
Corrections and comments
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Authors and funding
26 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.