Dear colleagues,

The SPAAM Community is offering a new 5 day virtual summer school course
sponsored by the Werner Siemens Foundation:*Introduction to Ancient Metagenomics*.

Date and schedule: Online from Monday 1st to Friday 5th of August from
09:00 to 17:00 (CEST, Leipzig time zone).

Organisers: Dr. Christina Warinner (Harvard University, Max Planck
Institute for Evolutionary Anthropology) and 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,
Megan Michels, Alina Hiß, Clemens Schmid, Maxime Borry (and more TBC)

Course Overview:
Ancient metagenomics applies cutting-edge metagenomic methods to the
degraded DNA content of archaeological 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
anthropogenic 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*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 assembly. 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) or a certificate of completion
(Max Planck - Harvard Research Center, MHAAM).

*Syllabus*:

DAY 1

   * Lecture: Introduction to NGS data
   * Practical 1: BareBonesBash 1
   * Practical 2: BareBonesBash 2
   * Round table: Introductions

DAY 2

   * Lecture: Introduction to ancient DNA
   * Practical 1: Bytesize git
   * Practical 2: ancientMetagenomeDir
   * Practical: nf-core/eager
   * Round table: Project organisation

DAY 3

   * Lecture: Introduction to metagenomics
   * Practical 1: Introduction to R and the tidyverse
   * Practical 2: Taxonomic profiling, OTU tables and visualisation
   * Round table: Taxonomic classifiers

DAY 4

   * Lecture Introduction to microbial genomics
   * Practical 1: Genome mapping
   * Practical 2: Genome assembly
   * Roundtable: Databases

DAY 5

   * Lecture Evolutionary biology
   * Practical 1: Phylogenomics
   * Practical 2: Functional genomics
   * Round table: Workshop review


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 19 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
([log in to unmask]) or Christina Warinner
([log in to unmask])

Best regards
Christina and James

-- 
James A. Fellows Yates

Microbiome Sciences Group, Dept. of Archaeogenetics
Max Planck Institute for Evolutionary Anthropology

Dept. of Paleobiotechology
Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

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