NGS, raw read pre-processing, quality control, and read mapping
All data and files for this section can be found in the EBI training FTP.
Overview of NGS technology
Trainers: Chiara Batini and Pille Hallast
Overview: This lecture provides an overview of NGS technologies and provides both a theoretical and historical perspective to sequencing technology and data.
Learning outcomes:
By the end of this session you will be able to:
- List the main technologies used to sequence lengths of genes and genomes
Materials:
Quality control
Trainers: Charles Solomon and Chiara Batini
Overview: This lecture and practical gives an overview of sequencing file formats and how to interpret quality of sequencing before proceeding to downstream processing.
Learning outcomes:
By the end of this session you will be able to:
- List the file formats common within sequencing experiments and pipelines
- Interpret the quality of sequencing experiments’ initial results
Materials:
- ‘Data quality control’ slides
- Practical session materials: including Handbook and Recommendations for practicals
- Material for practicals:
Read mapping
Trainers: Charles Solomon and Chiara Batini
Overview: This lecture covers the usage of fastq/fastqc files in alignment to a reference genome, the output files SAM/BAM and the downstram processes thereafter. The practical provides training in how to you use samtools, bwa, picard and other tools to align reads to a reference genome.
Learning outcomes:
By the end of this session you will be able to:
- Describe the usage of sequencing output files in alignment to a reference genome
- Use various tools to align reads to a reference genome
Materials: