Module: Sequence Analysis Basics

This modules covers the basics of sequence analysis, including Quality Control (QC), mapping, and genome assembly.

In this sesssion, we will walk you through the basics of quality checking your sequencing data. This session consists of a lecture followed by a hands-on tutorial.

Quality Control (Lecture)

Description:

This lecture goes over the concepts involved in assessing the quality of your sequencing data.
Length: 40 minutes
Captions: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
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Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

Quality Control (Tutorial)

Description:

In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.
Length: 1 hour 10 minutes
Captions: Bérénice Batut, Nadia Goué, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

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In this sesssion, we will walk you through the basics of mapping your sequencing data to a reference genome. This session consists of a lecture followed by a hands-on tutorial.

Mapping (Lecture)

Description:

This lecture covers the basic concepts involved in mapping sequencing reads to a reference genome.
Length: 10 minutes
Captions: Daniel Blankenberg
Created: 15 February 2021
Materials:
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Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

Mapping (Tutorial)

Description:

In this tutorial you will map sequencing data to a reference genome, and explore the mapped reads in a genome browser.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
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Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

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This session provides an introduction to Genome Assembly

An Introduction to Genome Assembly (Lecture)

Description:

This lecture walks you through the basic concepts involved in assembling a genome from short-read sequencing data.
Length: 25 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
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Learning Objectives:
  • assemble some paired end reads using Velvet
  • examine the output of the assembly.
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Speaker

Chloroplast genome assembly (Lecture & Tutorial)

Description:

In this tutorial, you will assemble a chloroplast genome using a combination of short and long read data.
Length: 35 minutes
Captions: Anna Syme
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Assemble a chloroplast genome from long reads
  • Polish the assembly with short reads
  • Annotate the assembly and view
  • Map reads to the assembly and view
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Speaker

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