ECCVID - 653 - Topolsky Ivan - Applying V-pipe to SARS-CoV-2 скачать в хорошем качестве

ECCVID - 653 - Topolsky Ivan - Applying V-pipe to SARS-CoV-2

Applying V-pipe to SARS-CoV-2 https://cbg-ethz.github.io/V-pipe/ Background: Next-generation sequencing (NGS) of viral genomes is now the method of choice for analysing the diversity of intra- and inter- host virus populations, including epidemiological studies and individual treatment optimization in clinical virology. V-pipe provides a data analysis workflow for clinical applications of NGS data obtained from viral genomes. The pipeline assesses data quality, performs read alignment and infers intra-sample viral genomic diversity: single-nucleotide variations and haplotype assembly. In this oral presentation we show the latest development of our SIB (Swiss Institute of Bioinformatics) resource: V-Pipe. Methods: V-pipe is used to fully automate the processing of raw reads data produced by sequencing effort on samples obtained from SARS-CoV-2 viral tests done by Viollier AG in Basel. Sequencing has been performed at the Genomics Facility Basel, on an Illumina MiSeq machine, and our team was provided with the raw reads over an OpenBIS database. In addition to that, our team has also focused on the visualization and reporting generation to assist the analysis of intra-host and whole cohort diversity of virus variations. Results: V-pipe has performed quality checks are automatically at each step of the pipeline. Passing sequences have then been uploaded to repositories such as GISAID enabling downstream phylogenetic analysis by other members of the task force such as the Swiss build of Nextstrain. These results are available at: https://ncs-tf.ch/en/nextstrain. V-pipe has also produced reports that enable easy exploration of SNV and visually situating them in regions of interest. The reports are produced in an HTML and JavaScript format, making it easy for the researcher to display them into a standard web browser. Conclusions: V-pipe has proven an useful SIB resource when applied to SARS-CoV-2. Further informations about this application of the pipeline (including tutorials) can be found on the dedicate SARS-CoV-2 sub-page of V-pipe's website: https://cbg-ethz.github.io/V-pipe/sar... Further informations about V-pipe are available at: https://cbg-ethz.github.io/V-pipe/ Presenter: Ivan Topolsky Authors: Susana Posada Céspedes Monica Dragan Kim Philipp Jablonski Pedro Falé Ferreira Aashil Batavia Prof. Niko Beerenwinkel Slidedeck: https://drive.sib.swiss/index.php/s/w... The work presented in the oral presentation has been financed by the Swiss Institute of Bioinformatics (SIB) and by ETH Zurich. The Illumina MiSeq illustration used in the slide is used under license from Illumina, Inc. All Rights Reserved.