A standardized pipeline for assembly and annotation of African swine fever virus genome

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationUnited States Department of Agricultureen
cg.contributor.affiliationAustralian Centre for Disease Preparednessen
cg.contributor.affiliationCanadian Food Inspection Agencyen
cg.contributor.affiliationOak Ridge Institute for Science and Educationen
cg.contributor.affiliationFriedrich Loeffler Instituten
cg.contributor.affiliationSwedish Veterinary Agencyen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationUniversity of Pretoriaen
cg.contributor.affiliationChinese Academy of Agricultural Sciencesen
cg.contributor.affiliationChulalongkorn Universityen
cg.contributor.affiliationPirbright Instituteen
cg.contributor.affiliationMakerere Universityen
cg.contributor.affiliationUnited Kingdom Health Security Agencyen
cg.contributor.affiliationBiomathematics and Statistics Scotlanden
cg.contributor.donorUnited States Department of Agricultureen
cg.contributor.donorBiotechnology and Biological Sciences Research Council, United Kingdomen
cg.creator.identifierLucilla Steinaa: 0000-0003-3691-3971
cg.creator.identifierAnna Lacasta: 0000-0001-8381-9844
cg.howPublishedFormally Publisheden
cg.identifier.dataurlhttps://github.com/Global-ASFV-Research-Alliance/ASFV_Pipeline/tree/mainen
cg.identifier.doihttps://doi.org/10.3390/v16081293en
cg.isijournalISI Journalen
cg.issn1999-4915en
cg.issue8en
cg.journalVirusesen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaResilient Agrifood Systems
cg.subject.ilriASFen
cg.subject.impactAreaNutrition, health and food security
cg.subject.impactPlatformNutrition, Health and Food Security
cg.subject.sdgSDG 2 - Zero hungeren
cg.volume16en
dc.contributor.authorSpinard, E.en
dc.contributor.authorDinhobl, M.en
dc.contributor.authorErdelyan, C.N.G.en
dc.contributor.authorO’Dwyer, J.en
dc.contributor.authorFenster, J.en
dc.contributor.authorBirtley, H.en
dc.contributor.authorTesler, N.en
dc.contributor.authorCalvelage, S.en
dc.contributor.authorLeijon, M.en
dc.contributor.authorSteinaa, Lucillaen
dc.contributor.authorO'Donnell, V.en
dc.contributor.authorBlome, S.en
dc.contributor.authorBastos, A.en
dc.contributor.authorRamirez-Medina, E.en
dc.contributor.authorLacasta, Annaen
dc.contributor.authorStåhl, K.en
dc.contributor.authorQiu, H.en
dc.contributor.authorNilubol, D.en
dc.contributor.authorTennakoon, C.en
dc.contributor.authorMasembe, C.en
dc.contributor.authorFaburay, B.en
dc.contributor.authorAmbagala, A.en
dc.contributor.authorWilliams, D.en
dc.contributor.authorRibeca, P.en
dc.contributor.authorBorca, M.V.en
dc.contributor.authorGladue, D.P.en
dc.date.accessioned2024-08-15T14:54:44Zen
dc.date.available2024-08-15T14:54:44Zen
dc.identifier.urihttps://hdl.handle.net/10568/151696
dc.titleA standardized pipeline for assembly and annotation of African swine fever virus genomeen
dcterms.abstractObtaining 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.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademicsen
dcterms.audienceScientistsen
dcterms.available2024-08-13
dcterms.bibliographicCitationSpinard, E., Dinhobl, M., Erdelyan, C.N.G., O’Dwyer, J., Fenster, J., Birtley, H., Tesler, N., Calvelage, S., Leijon, M., Steinaa, L., O'Donnell, V., Blome, S., Bastos, A., Ramirez-Medina, E., Lacasta, A., Ståhl, K., Qiu, H., Nilubol, D., Tennakoon, C., Masembe, C., Faburay, B., Ambagala, A., Williams, D., Ribeca, P., Borca, M.V. and Gladue, D.P. 2024. A standardized pipeline for assembly and annotation of African swine fever virus genome. Viruses 16(8): 1293.en
dcterms.extent1293en
dcterms.issued2024-08-13
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherMDPI AGen
dcterms.subjectafrican swine fever virusen
dcterms.subjectgenomicsen
dcterms.typeJournal Article

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