Course information

Course title
Manipulation of NGS Data for Genomic and Population Genetics Analyses
University / Organization
Transmitting Science
City
Capellades (Barcelona)
Country
Spain
Academic level
Both Msc and PhD
Language
English
School
Transmitting Science
Address
Course director
Course lecturer(s)
Dr. François Sabot (Institute of Research for Development, France) and Dr. Christine Tranchant-Dubreuil (Institute of Research for Development, France)
Course aim
Program Monday, June 17th, 2019. Introduction to NGS sequencing platforms. Introduction to basic command lines. Basic raw data manipulations (counting sequences, listing files). Tuesday, June 18th, 2019. Raw data QC & Cleaning. Introduction to TOGGLe, a NGS pipeline framework. Mapping: principle, tools, execution. Mapping: cleaning, data control, realigning, duplicates marking. Wednesday, June 19th, 2019. SNP calling: raw calling, cleaning calling, filtering. VCF manipulations: filtering on MAF, heterozygosity… Impact of SNPs on genes. Population genomics using sNMF. Thursday, June 20th, 2019. Context-based analyses. Piping large scale analyses for multiple samples using TOGGLe. Testing new tools and different conditions to answer different biological questions. Questions.
Course contents / programme
Required Knowledge and preparation
Teaching methods
Assessment
Course type
Seminar
Consecutive days
Yes
Online course
No
Duration (net days)
June 17th-20th, 2019
Credits
Course fee
Direct e-mail to register
Paper submission required?
Logo of institution
front approval