Course material for:

NGS for evolutionary biologists: from basic scripting to variant calling

Biblioteca, Consiglio Nazionale delle Ricerche
via P. Castellino 111
80131 Naples, Italy

May 2-6, 2016

course announcement
course program

Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomes and identify mutations relevant for the study of both evolutionary questions and diagnosis and therapy. This course runs over five days focusing on variant analysis of NGS data and is addressed to wet lab scientists with little or no previous knowledge of the use of a command line, statistical computing packages, and programming. Participants are immersed in the experience of running a complete NGS data analysis work-flow, from the retrieval of raw data from bioinformatics resources, to the downstream analysis of the processed data.

This repository is for the course materials and it is organized as follows:

Days	Lessons	Tutorials
day 1	Unix/Linux command line	Connection to remote server, Practical Unix and Basic R ( intro, basic, data frames, ggplot), and NGS and Population Genomics
day 2	NGS platforms and Data format an Quality Control	Data QC
day 3	Mapping and BAM refinement	Mapping
day 4	Variant Calling	SNP calling, SV calling and Filtering
days 2-5	Practical Projects	Project 1 and Project 2