Welcome to the de.NBI - CeBiTec Nanopore Workshop 2020!¶
Best Practice and SARS-CoV-2 applications¶
Welcome to the three-day nanopore Hands-On training course. This tutorial will guide you through the typical steps of the analysis of ONT sequencing data ranging from basecalling, quality assessment over assembly to sequence polishing and finally assembly evaluation. A focus in this workshop is on the analysis of Nanopore sequenced SARS-CoV-2 genomes and a suitable workflow for resequencing based on the ARTIC bioinformatics protocol.
- Connect to your virtual machine
- The Tutorial Data Sets
- Basecalling
- Data Quality Assessment
- Recap Day 1
- Assembly
- Assembly with canu
- Assembly with canu(2)
- Assembly with canu(3)
- Assembly evaluation with QUAST
- Assembly evaluation with QUAST(2)
- Assembly Graph inspection with Bandage
- Get and inspect the WGS dataset
- Assembly of WGS dataset
- Assembly with WGS dataset(2)
- WGS Assembly evaluation with QUAST
- WGS Assembly evaluation with QUAST(2)
- WGS Assembly Graph inspection with Bandage
- Quality control by mapping
- Quality control by mapping(2)
- Assembly polishing
- Recap Day 2 / Preparations Day 3
- ARTIC pipeline
- Outlook