Paleogenomics - from metagenomics to phylogenomics

Dates

16-20 November 2020

 

 

Due to the COVID-19 outbreak, this course will be held online

 

Overview

This course will introduce biologists to the main bioinformatics tools for the analysis of Next Generation Sequencing (NGS) data from ancient samples. Through a series of theoretical and practical hands-on sessions, this course will give you a clear understanding of the most common bioinformatics methods adopted in a wide range of paleogenomics projects. During the course we will cover various steps from metagenomics screening of ancient samples and taxonomical assignment, to NGS reads mapping, authentication through post-mortem damage analysis, variants calling and filtering, and phylogenomics.

 

Participants will receive a basic introduction to NGS platforms and the main file formats used in the most common bioinformatics pipelines. Each day will consist of a mix of introductory lectures on the theoretical background of the programs that will be used, followed by hands-on exercises using command line tools performed by the participants under guided supervision. A best practice usage of state-of-the-art tools such as bwa, samtools, mapDamage, gatk, picard, will be provided during the course. Python and R will be used for data processing and visualization (no programming knowledge is needed).

 

 

Target Audience & ASSUMED BACKGROUND

The course is aimed at researchers from life sciences as well as humanities (MSc and PhD students, postdoctoral fellows, engineers, archaeologists, anthropologists) interested in learning how to process NGS sequence data. The hands-on sessions are targeted to beginners and more advanced users alike. The overall skills acquired at the end of the course can be applied to a wide range of projects, from metagenomics to genome resequencing of ancient as well as modern samples (including environmental samples). No specific background is needed to attend the course, some familiarity with genomic data is helpful.

 

 

STRUCTURE

The course material will be delivered over 5 days, in 10 half-day sessions. These lessons will build off of one another, and feature a mix of lecture and in-class exercises.

 

 

program

 

Monday, 9.30-17.30

 

 

Lecture:

 

- Presentation and course overview.

 

- Introduction to NGS and ancient DNA: the paleogenomic era

 

- Theoretical background on metagenomic analysis.

 

 

Hands-on:

 

- Introduction to Unix: basic and advanced command line concepts.

 

- Metagenomic screening of ancient samples (e.g. Metaphlan, Kraken, Krona)

 


 


Instructor

 

 

Dr. Claudio Ottoni

 

 

 

 

Dr. Amine Namouchi

 

Cost overview

 

Package 1

Course material

 

          530 € (VAT included)


Please click HERE to get all the information about our packages.

Registration deadline: 16th October 2020

Cancellation Policy:

 

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.