Characterising genomic and epigenomic variants in tumour-normal research samples: data analysis

During this Knowledge Exchange, Philipp Rescheneder, Director, Genomic Applications Bioinformatics, and Andrea Talenti, Bioinformatics Workflow Developer,  described how to analyse genomic and epigenomic variation in tumour-normal nanopore sequencing data from cancer research samples. Following on from the 'How to perform tumour-normal sequencing' masterclass, Philipp began by introducing how long nanopore sequencing reads of native DNA can be used to accurately identify structural variants (SVs), methylation differences, single nucleotide variants (SNVs), and copy number variants (CNVs) between matched tumour-normal research samples. He also explained how long nanopore sequencing reads can be used to assign variants to a haplotype.

Andrea then described how data from a single sequencing run can be used to detect SVs, methylation, and SNVs using the dedicated EPI2ME analysis pipeline, wf-somatic-variation, from Oxford Nanopore. Starting from the beginning and including everything needed to begin your analyses, Andrea demonstrated how to run a dataset using the command-line interface and explain both the basic and advanced features of the analysis pipeline, to suit different levels of expertise. He also highlighted the output files and reports generated at the end of the analysis, and discussed upcoming developments.