Oxford Nanopore Technologies (ONT) are revolutionising DNA sequencing as they allow researchers to go from sample to sequence in hours and sequence extremely long DNA molecules. Consequently, a large number of tools have been developed for base calling, data handling, read mapping, de novo assembly and variant discovery for Nanopore data. These tools often can be difficult to install or use. In addition, users face the computational challenges related to the analysis of very long reads. In this 2-part CyVerse Focus Forum Webinar series, we will survey and quickly demonstrate the different computational tools that are available for Nanopore data analysis in the CyVerse Discovery Environment. Part 1 will focus on NanoDJ (https://github.com/genomicsITER/NanoDJ) which is a Jupyter notebook integration of tools in CyVerse VICE for simplified manipulation and assembly of DNA sequences produced by Nanopore. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly. In Part 2, we will highlight a variety of non-interactive apps that are available in the CyVerse Discovery Environment for data manipulation, trimming, mapping, assembly and variant detection of Nanopore data.
Presenter: Upendra Devisetty, CyVerse science analyst
Slides and Other Materials:
Presenter: Jawon Song, CyVerse-TACC