WORKSHOPS
SPAAM Summer School
We are very proud to announce a new 5-day intensive Summer School course sponsored by the SPAAM-Community and the Werner Siemens Foundation: “Introduction to Ancient Metagenomics”!
Practical Introduction to Ancient Metagenomics! Learn how to run a project analysis from A-Z!
DATE AND SCHEDULE:
Online from Monday 1st to Friday 5th of August 2022 from 09:00 to 17:00 (CEST, Leipzig time zone).
ORGANISERS:
Dr. Christina Warinner (Harvard University, Max Planck Institute for Evolutionary Anthropology); James Fellows Yates (Max Planck Institute for Evolutionary Anthropology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute).
INSTRUCTORS:
Dr. Aida Andrades Valtueña, Dr. Thiseas C. Lamnidis, Dr. Arthur Kocher, Dr. Alex Hübner, Dr. Irina Velsko, Dr. Alexander Herbig, Dr. Christina Warinner, James Fellows Yates, Megan Michel, Alina Hiß, Clemens Schmid, Maxime Borry (and more TBA)
COURSE OVERVIEW:
Ancient metagenomics applies cutting-edge metagenomic methods to the degraded DNA content of archaeo- logical and paleontological specimens. The rapidly growing field is currently uncovering a wealth of novel information for both human and natural history, from identifying the causes of devastating pandemics such as the Black Death, to revealing how past ecosystems changed in response to long-term climatic and anthropo- genic change, to reconstructing the microbiomes of extinct human relatives. However, as the field grows, the techniques, methods, and workflows used to analyse such data are rapidly changing and improving.
In this one-week hands-on summer school (block praktikum) we will go through the main steps of ancient metagenomic bioinformatic workflows, familiarising students with the command line, demonstrating how to process next-generation-sequencing (NGS) data, and showing how to perform de novo metagenomic assem- bly. Focusing on host-associated ancient metagenomics, the course consists of a combination of lectures and hands-on exercises, allowing participants to become familiar with the types of questions and data researchers work with. Round table discussions with experts at each stage of the workflow will be held to allow participants to get advice on their own projects and research.
By the end of the course, participants will have an understanding of how to effectively carry out the major bioinformatic components of an ancient metagenomic project in an open and transparent manner. Attendees will be eligible for ECTS points (awarded by the JSMC Graduate School, Friedrich-Schiller University, Germany) and a certificate of completion (Max Planck – Harvard Research Center, MHAAM).
TOPICS: DAY 1: Introduction to NGS data; BareBonesBash. DAY 2: Introduction to ancient DNA; Bytesize git; ancientMetagenomeDir; nf-core/eager; Project organisation. DAY 3: Introduction to metagenomics; Introduction to R and the tidyverse; Taxonomic profiling, OTU tables and visualisation; Taxonomic classifiers; DAY 4: Introduction to microbial genomics; Genome mapping; Genome assembly; Databases; DAY 5: Evolutionary biology; Phylogenomics; Functional genomics
ELIGIBILITY:
The course is aimed at masters students and early-stage PhD students, to a maximum of 25 participants. Course instruction will take place online.
APPLICATIONS:
Applications are open from April 29 to June 1 2022. To apply, please visit our website:
https://spaam-community.github.io/wss-summer-school/
For questions or more information, contact James Fellows Yates (james_fellows_yates@eva.mpg.de) or Christina Warinner (warinner@fas.harvard.edu)