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
Target audience: Students
Resource type: e-learning
Version: 44
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: 2024-10-27
Date published: 2016-10-04
Contributors: Alexandre Cormier, Anthony Bretaudeau, Bérénice Batut, Erasmus+ Programme, Erwan Corre, Laura Leroi, Maria Doyle, Stéphanie Robin
Scientific topics: Sequence analysis
Activity log
