0000000001317690
AUTHOR
Dana E. Rollison
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
Abstract Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. Results We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify kno…
Generation of a novel next-generation sequencing-based method for the isolation of new human papillomavirus types
Abstract With the advent of new molecular tools, the discovery of new papillomaviruses (PVs) has accelerated during the past decade, enabling the expansion of knowledge about the viral populations that inhabit the human body. Human PVs (HPVs) are etiologically linked to benign or malignant lesions of the skin and mucosa. The detection of HPV types can vary widely, depending mainly on the methodology and the quality of the biological sample. Next-generation sequencing is one of the most powerful tools, enabling the discovery of novel viruses in a wide range of biological material. Here, we report a novel protocol for the detection of known and unknown HPV types in human skin and oral gargle …
Additional file 2 of PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
Additional file 2: Supplementary Data 1. Info file description. Supplementary Data 2. Details of the workflow steps. Supplementary Data 3. Description of output files format. Supplementary Data 4. Sample collection, preparation, and sequencing
Additional file 1 of PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
Additional file 1: Supplementary Table S1. Info file. Supplementary Table S2. Taxonomic classification of the reads identified in the overall NGS experiment by MegaBlast alignment. Supplementary Table S3. Taxonomic classification of the reads identified in the overall NGS experiment by BlastN alignment. Supplementary Table S4. Taxonomic classification of the reads identified in the overall NGS experiment by RaxML-EPA. Supplementary Table S5. NGS metrics, summary classification of putative known and putative new virus based on the three methodologies. Supplementary Table S6. Putative known Papillomaviridae-related sequences detected in the NGS experiment. Supplementary Table S7. Performances…