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Human genome sequencing and analysis

In this course, we will introduce the latest updates and end-to-end workflows for sequencing the Human genome using the Kit V14 chemistry and performing analysis using the wf-human-variation workflow. This course will introduce and discuss kit V14 library preparation options, sequencing set up and analysis through the EPI2ME platform for the detection of SNPs, indels, SVs and methylation.

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Course overview

Human Genomics Planning

1 Introduction to Sequencing Human DNA with Nanopore
2 Introduction to sequencing devices
3 P2 Solo: First-time setup and hardware check
4 Library preparation: Extraction methods and sample handling
5 Library preparation: Quality control of input DNA or RNA
6 Improving sequencing yield

Human Genomics Preparation

7 Library preparation: Ligation sequencing kit
8 Kit V14 introduction and overview
9 Kit V14 performance
10 MinKNOW: The graphical user interface (GUI)
11 Flow cell handling

Human Genomics Sequencing

12 A practical demonstration of priming and loading a flow cell
13 MinKNOW: Setting up a new experiment
14 MinKNOW Configuration for Kit 14
15 Methylation Detection On MinKNOW
16 MinKNOW: Live basecalling and output folder structure
17 MinKNOW: Assessing your run
18 Introduction: Real-time analysis

Human Genomics Analysis

19 Introduction to data generation and sequencing output for analysis
20 Introduction to data analysis solutions
21 Methylation Detection: Sample to Answer Workflow Overview
22 Data Analysis: EPI2ME Labs introduction
23 EPI2ME Labs: wf-human-variation Platform Demo
24 Introduction to EPI2ME Labs workflows
25 EPI2ME Labs Nextflow Workflows demonstration
26 Introduction to SNP and indel detection
27 Introduction to structural variation detection

Library preparation: Extraction methods and sample handling

6 min
Learning objectives
  • Deciding on the correct sample extraction step based on experimental aim
  • Concepts to consider during your sample extraction steps
  • The importance of correctly quantifying the extracted material
  • Review of some general best practices
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