NanoHIV: a bioinformatics pipeline for producing accurate, near full-length HIV proviral genomes sequenced using the Oxford Nanopore technology

Simple item page
dc.contributor.authorWright, Imogen A.en_ZA
dc.contributor.authorDelaney, Kayla E.en_ZA
dc.contributor.authorKatusiime, Mary Grace K.en_ZA
dc.contributor.authorBotha, Johannes C.en_ZA
dc.contributor.authorEngelbrecht, Susanen_ZA
dc.date.accessioned2023-05-11T13:22:43Zen_ZA
dc.date.available2023-05-11T13:22:43Zen_ZA
dc.date.issued2021-09en_ZA
dc.descriptionCITATION: Wright, I.A.; Delaney, K.E.; Katusiime, M.G.K.; Botha, J.C.; Engelbrecht, S.; Kearney,M.F.; van Zyl, G.U. 2021. NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology. Cells , 10, 2577. doi.10.3390/cells10102577en_ZA
dc.descriptionThe original publication is available at: mdpi.comen_ZA
dc.description.abstractHIV-1 proviral single-genome sequencing by limiting-dilution polymerase chain reaction (PCR) amplification is important for differentiating the sequence-intact from defective proviruses that persist during antiretroviral therapy (ART). Intact proviruses may rebound if ART is interrupted and are the barrier to an HIV cure. Oxford Nanopore Technologies (ONT) sequencing offers a promising, cost-effective approach to the sequencing of long amplicons such as near full-length HIV-1 proviruses, but the high diversity of HIV-1 and the ONT sequencing error render analysis of the generated data difficult. NanoHIV is a new tool that uses an iterative consensus generation approach to construct accurate, near full-length HIV-1 proviral single-genome sequences from ONT data. To validate the approach, single-genome sequences generated using NanoHIV consensus building were compared to Illumina® consensus building of the same nine single-genome near full-length amplicons and an average agreement of 99.4% was found between the two sequencing approaches.en_ZA
dc.description.versionPublisher’s versionen_ZA
dc.format.extent12 pagesen_ZA
dc.identifier.citationWright, I.A.; Delaney, K.E.; Katusiime, M.G.K.; Botha, J.C.; Engelbrecht, S.; Kearney,M.F.; van Zyl, G.U. 2021. NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology. Cells , 10, 2577. doi.10.3390/cells10102577en_ZA
dc.identifier.issn2073-4409 (online)en_ZA
dc.identifier.otherdoi.10.3390/cells10102577en_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/126904en_ZA
dc.language.isoen_ZAen_ZA
dc.publisherMDPIen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectHIVen_ZA
dc.subjectNanoporeen_ZA
dc.subjectProviralen_ZA
dc.subjectConsensusen_ZA
dc.subjectSingle-genomeen_ZA
dc.titleNanoHIV: a bioinformatics pipeline for producing accurate, near full-length HIV proviral genomes sequenced using the Oxford Nanopore technologyen_ZA
dc.typeArticleen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
imogen_nano_2021.pdf
Size:
735.58 KB
Format:
Adobe Portable Document Format
Description:
download article
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Research Articles (Medical Virology)