Table of Contents

Course Program

User's session

Monday

14:30-15:00 Registration

15:00-15:30 Course reception

15:30-16:00 Course Overview

16:30-17:00 Introduction to Linux Systems

Pablo Escobar
intro-linux-mda13.pdf

17:00-18:00 Introduction to NGS Technologies for Variation Studies

Javier Santoyo - Introduction to NGS technologies
Youtube videos:

Tuesday

09:30-11:00 Quality Control for NGS Raw Data

Francisco García - Quality Control, practical session with solutions, code.txt.

Software: FastQC, Fastx-Toolkit, HPC fastq

File formats: fasta, fastq

11:30-13:00 Mapping NGS Reads for Genomic Studies

Ignacio Medina

Software: HPG aligner, BWA, Bowtie2, SAMtools

File formats: FASTQ, SAM/BAM

ngs-read-mapping-imedina-mda13.odp ngs-read-mapping-imedina-mda13.pdf

Human reference chromosome 20 and paired-end dataset from chromosome 20 available at: http://www.opencb.org/projects/hpg/doku.php?id=aligner:getting_started

13:00-14:30 Lunch

Will be held in the cafeteria of the CIPF.

14:30-16:00 Quality control for Mapping

Francisco Javier López

Software: QualiMap

map_qc.pdf

igv.pdf

16:30:18:00 Visualization of mapped reads

Francisco Javier López

Software: BAM viewer, IGV

21:00 Gala Dinner

See details.

Wednesday

09:30-11:00 Variant Calling SNPs

Jorge Jiménez

Software: GATK

File formats: VCF

variant_calling.pdf

Variant calling hands on

11:30-13:00 Variant Calling IN-DELS

Jorge Jiménez

Software: GATK

File formats: VCF

13:00-14:30 Lunch

Will be held in the cafeteria of the CIPF.

14:30-16:00 Variant Annotation

Marta Bleda

Software: HPG variant effect

PRESENTATION PDF: mbleda-mda13-variant_annotation.pdf

PRESENTATION ODP: mbleda-mda13-variant_annotation.odp

Example VCF: chb.exon.2010_03.sites.vcf.zip

16:30:18:00 Association Studies

Ignacio Medina, Cristina Yenyxe, Marta Bleda

Software: HPG Variant

File formats: VCF, ped

gwas-mda-13.odp gwas-mda-13.pdf

Thursday

09:30-11:00 Biological Data Bases

Ignacio Medina

cellbase-imedina-mda13.odp cellbase-imedina-mda13.pdf

Exercise file: gene_list.txt

11:30-13:00 Gene-Set Methodologies for NGS Data

David Montaner

gene_set_ngs.odp

gene_set_ngs.pdf

gene_set_ngs.txt

13:00-14:30 Lunch

Will be held in the cafeteria of the CIPF.

Developer's session

Thursday

14:30-16:00 Introduction to software libraries and technologies

Ignacio Medina

dev-intro-imedina-mda13.odp dev-intro-imedina-mda13.pdf

16:30-18:00 HPG Aligner and sequence alignment libraries

Joaquín Tárraga

hpg-aligner-jtarraga-mda13.pdf hpg-aligner-jtarraga-mda13.odp

Friday

09:30-11:00 HPG Variant architecture and libraries

Cristina Yenyxe

hpg-variant-developers.pdf

11:30-13:00 HTML5 visualization: Genome Maps and CellBrowswer

Francisco Salavert

13:00-14:30 Lunch

Will be held in the cafeteria of the CIPF.

14:30:16:00 Closing