e-learning
Quality Control
Abstract
During sequencing, the nucleotide bases in a DNA or RNA sample (library) are determined by the sequencer. For each fragment in the library, a sequence is generated, also called a read, which is simply a succession of nucleotides.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How to perform quality control of NGS raw data?
- What are the quality parameters to check for a dataset?
- How to improve the quality of a dataset?
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
Licence: Creative Commons Attribution 4.0 International
Keywords: Sequence analysis, deutsch, español, italiano
Target audience: Students
Resource type: e-learning
Version: 49
Status: Active
Prerequisites:
Introduction to Galaxy Analyses
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
Date modified: 2026-03-30
Date published: 2016-10-04
Authors: 
Alexandre Cormier, Anthony Bretaudeau, Bérénice Batut, Cameron Hyde, Erwan Corre, Laura Leroi, Maria Doyle, Stéphanie Robin
Contributors: Matthias Bernt, Alexandre Cormier, Anika Erxleben, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Natalie Kucher, Simon Bray, Swathi Nataraj, William Durand, Björn Grüning, Bérénice Batut, Cristóbal Gallardo, Helena Rasche, Maria Doyle, Mateo Boudet, Nicola Soranzo, Saskia Hiltemann, Teresa Müller, Wolfgang Maier
Scientific topics: Sequence analysis
Activity log
