Alejandro R. Gener
ProvirusNanopore sequencingGenomeSequence assemblyPlasmidMinionContext (language use)Human immunodeficiency virus (HIV)Full coverageFASTQ formatComputer scienceDNA sequencingRNA splicingContigRNAComputational biologyAmpliconBiology
Publications 3
#1Alejandro R. GenerH-Index: 2
#2Wei Zou (LANL: Los Alamos National Laboratory)
Last. Paul E. Klotman (BCM: Baylor College of Medicine)H-Index: 63
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Objective: To compare long-read nanopore DNA sequencing (DNA-seq) with short-read sequencing-by-synthesis for sequencing a full-length (e.g., non-deletion, nor reporter) HIV-1 model provirus in plasmid pHXB2_D. Design: We sequenced pHXB2_D with long- and short-read DNA-seq, evaluating sample variability with resequencing (sequencing and mapping to reference HXB2) and de novo viral genome assembly. Methods: We prepared pHXB2_D for long-read nanopore DNA-seq, varying DNA polymerases Taq (Sigma-Ald...
#1Alejandro R. Gener (BCM: Baylor College of Medicine)H-Index: 2
#2Jason T. Kimata (BCM: Baylor College of Medicine)H-Index: 19
Objective: To evaluate native RNA sequencing for sequencing HIV-1 viral genomes. Methods: Fifteen HIV-1 strains were processed with Direct RNA Sequencing (SQK-RNA002) library kits and sequenced on MinION Mk1B devices with RevD flow cells (Oxford Nanopore Technologies (ONT), Oxford, UK). Raw reads were converted to FASTQ, aligned to reference sequences, and assembled into contigs. Multi-sequence alignments of the contigs were generated and used for cladistics analysis. Results: We sequenced full-...
2 CitationsSource
ABSTRACT Objective(s) To evaluate nanopore DNA sequencing for sequencing full-length HIV-1 provirus. Design I used nanopore sequencing to sequence full-length HIV-1 from a plasmid (pHXB2). Methods pHXB2 plasmid was processed with the Rapid PCR-Barcoding library kit and sequenced on the MinION sequencer (Oxford Nanopore Technologies, Oxford., UK). Raw fast5 reads were converted into fastq (base called) with Albacore, Guppy, and FlipFlop base callers. Reads were first aligned to the reference with...
3 CitationsSource