About the course

Main instructors:

Luca Cozzuto

Toni Hermoso

Julia Ponomarenko

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Dates, time, location

  • Dates:

  • Location:

Program

Outline

This NGS Quality Control (QC) course will train participants to run FASTQC on short reads obtained with Illumina and interpret the quality control parameters offered by this tool.

Learning objectives

  • Know the main steps of a library preparation in DNA-seq and RNA-seq, the bias introduced in each of this and solutions to avoid them

  • Learn how the main sequencing technologies works (Illumina for short reads and Nanopore for long reads).

  • Execute/Run the main quality control tools for raw data (FASTQC/NanoPlot and FASQ-Screen) obtained for short and long reads.

  • Understand the FASTQ format and interpret the Quality Control report offered by theese tools.

  • Aggregate the QC reports of different tools and samples with MULTIQC.

  • Execute and learn about the preprocessing tools for adapter and low quality reads removal (TRIMMOMATIC, Cutadapter, Sickle, Fastp).

Prerequisite / technical requirements

Being comfortable working with the CLI (command-line interface) in a Linux-based environment (Introductory courses to CLI may be recommended)git .