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[Maize] Course NGS data for Genomic and population genetic analyses, May 14-17, Barcelona, Spain

soledad.esteban via maize%40net.bio.net (by soledad.esteban from icp.cat)
Wed Feb 14 09:45:08 EST 2018

Dear colleagues, This course might be of interest for the members of this list: MANIPULATION OF NGS DATA FOR GENOMIC AND POPULATION GENETICS ANALYSES.

Date: May 14th-17th, 2018, Barcelona (Spain).


PLACE: Capellades, Barcelona.


INSTRUCTORS: Dr. François Sabot (Institute of Research for Development, France) and Dr. Christine Tranchant-Dubreuil (Institute of Research for Development, France)



- Monday, May 14th, 2018.

Introduction to NGS sequencing platforms.

Introduction to basic command lines.

Basic raw data manipulations (counting sequences, listing files).

- Tuesday, May 15th, 2018.

Raw data QC & Cleaning.

Introduction to TOGGLe, a NGS pipeline framework.

Mapping: principle, tools, execution.

Mapping: cleaning, data control, realigning, duplicates marking.


- Wednesday, May 16th, 2018.

SNP calling: raw calling, cleaning calling, filtering.

VCF manipulations: filtering on MAF, heterozygosity…

Impact of SNPs on genes.

Population genomics using sNMF.

- Thursday, May 17th, 2018.

Context-based analyses.

Piping large scale analyses for multiple samples using TOGGLe.

Testing new tools and different conditions to answer different biological questions.


With best regards


Soledad De Esteban-Trivigno
Institut Català de Paleontologia Miquel Crusafont (ICP)

Campus de la Universitat Autònoma de Barcelona

Cerdanyola del Vallès (Barcelona). Spain


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