Table of Contents
Day 1
11:00 – 11:30 Course presentation.
- Joaquin Dopazo.
11:30 – 12:00 Introduction to Linux command line.
- Pablo Escobar
12:00 – 13:00 Introduction to NGS technologies.
- Javier Santoyo
13:00 – 13:30 Computing infrastructure for NGS analyses.
- Pablo Escobar.
13:30 – 15:00 Lunch break
Will be held in the cafeteria of the CIPF.
15:00 – 16:30 NGS data preprocessing concepts.
- Jose Carbonell.
Handling sequence files.
Fasta and fastq file formats overview.
Encoding quality metrics.
Quality control tools.
Bias detection.
Sequence filtering.
16:30 – 17:00 Coffee break
Will be held in the cafeteria of the CIPF.
17:00 – 18:30 NGS data preprocessing practical session.
- Jose Carbonell and Francisco Garcia.
Hands on session with FastQC and FastX-Toolkit programs.
21:00 GALA DINNER
- See details here: course_dinner.pdf
Day 2
10:00 – 11:30 Sequence alignment concepts.
- Enrique Vidal.
Reference genome as a concept.
NGS alignment programs and algorithms.
SAM/BAM and BED file formats overview.
Mapped reads visualization.
Quality control of the mapping.
Local realignment.
Computational needs.
11:30 – 12:00 Coffee break
Will be held in the cafeteria of the CIPF.
12:00 – 13:30 Sequence alignment practical session.
- Enrique Vidal and David Montaner.
Hands on session with alignment programs: bowtie, bwa and bfast.
Overview of quality control and visualization tools: bamQC, GATK and IGV.
Data handling with SAMtools.
13:30 – 15:00 Lunch break
Will be held in the cafeteria of the CIPF.
15:00 – 16:30 Variant calling in NGS experiments; concepts.
- Jorge Jimenez.
Variant types: SNPs and InDels.
Calling procedures and algorithms.
VCF file formats overview.
Introduction to the programs GATK, Annovar and Variant.
Variant filtering.
The problem of the missing data.
Variant annotation.
Data bases and data repositories: dbSNP and the 1000 genomes project.
16:30 – 17:00 Coffee Break
17:00 – 18:30 Variant calling practical session.
- Jorge Jimenez and Martina Marba.
Hands on with GATK, Annovar and IGV.
Day 3
9:30 – 11:30 Results interpretation.
- Jorge Jimenez and Enrique Vidal
A general view on how to interpret BIER analysis pipeline and results. Some remarks on experiment design.
11:30 – 12:00 Coffee break
Will be held in the cafeteria of the CIPF.
12:00 – 14:00 Some CIPF tools for visualization, variant characterization and pathway analysis.
- Patricia Sebastian and Marta Bleda
Variant, CellBase, Genome Maps and Pathway analysis.