Pablo Escobar
intro-linux-mda13.pdf

Javier Santoyo - Introduction to NGS technologies
Youtube videos:

• Illumina
• Solid
• FLX 454

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

Software: FastQC, Fastx-Toolkit, HPC fastq

File formats: fasta, fastq

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

Will be held in the cafeteria of the CIPF.

Francisco Javier López

Software: QualiMap

map_qc.pdf

igv.pdf

Francisco Javier López

Software: BAM viewer, IGV

See details.

Jorge Jiménez

Software: GATK

File formats: VCF

variant_calling.pdf

Variant calling hands on

Jorge Jiménez

Software: GATK

File formats: VCF

Will be held in the cafeteria of the CIPF.

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

Ignacio Medina, Cristina Yenyxe, Marta Bleda

Software: HPG Variant

File formats: VCF, ped

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

Ignacio Medina

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

Exercise file: gene_list.txt

David Montaner

gene_set_ngs.odp

gene_set_ngs.pdf

gene_set_ngs.txt

Will be held in the cafeteria of the CIPF.

Ignacio Medina

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

Joaquín Tárraga

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

Cristina Yenyxe

hpg-variant-developers.pdf

Francisco Salavert

Will be held in the cafeteria of the CIPF.