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
Address
Course director
Course lecturer(s)
Dr François Sabot (Institute of Research for Development, France) Dr Christine Tranchant-Dubreuil (Institute of Research for Development, France)
Course aim
Course contents / programme
Program 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. Questions.
Required Knowledge and preparation
Teaching methods
Assessment
Course type
Workshop
Consecutive days
Yes
Online course
No
Duration (net days)
May 14th-17th, 2018
Credits
Course fee
Direct e-mail to register
Paper submission required?
Logo of institution
front approval