Alignment and Genome assembly
All data and files for this section can be found in the EBI training FTP.
SAM/BAM file formats – BAM refinement, QC, and visualisation
Trainers: Chiara Batini
Overview: This lecture covers the SAM, BAM and CRAM file formats in more detail, with a focus on how to manipulate and interrogate SAM and BAM files.
Learning outcomes:
By the end of this session you will be able to:
- Describe the main features of SAM, BAM, CRAM files
- Interpret alignments through SAM and BAM files
- List the steps to refine, assess quality and visualise BAM files
- Recall GATK best practices for sequencing
Materials:
- ‘SAM/BAM file formats’ slides
- Practical session materials: including Handbook and Recommendations for practicals
Genome Assembly
Trainers: Victor Flores Lopez
Overview: This lecture covers the principles and purpose of genome assembly to understand its importance in genome bioinformatics.
Learning outcomes:
By the end of this session you will be able to:
- Describe the steps to assemble a genome
- Discuss the different strategies to perform genome assembly
Materials: