0000000000147893
AUTHOR
Magali Olivier
showing 3 related works from this author
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
2019
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…
Additional file 2 of PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
2020
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
2020
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…