A list of SPAAM commmunity projects
Here we provide a list of projects run by the SPAAM community that to assist in progressing the field.
- AncientMetagenomeDir and AMDirT
- Ancient Metagenomics Labs
- MINAS MIxS Checklist
- SPAAM Summer Schools
- SPAAM Blog
- SPAAMtisch
- Introduction to Ancient Metagenomics Textbook
- Little Book of Smiley Plots Book
AncientMetagenomeDir and AMDirT
AncientMetagenomeDir is a community curated resource of lists of all published shotgun-sequenced ancient metagenome samples. It is primarily meant to act as a reference guide to help point researchers toward any relevant public data for comparative analysis. It is hoped it will help researchers track growth and development of the field of ancient metagenomics over time.
AMDirT is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes. This tool provides ways to validate AncientMetagenomeDir submissions, explore and download sequencing data for ancient microbial and environmental (meta)genomes, and automatically prepare input samplesheets for a range of bioinformatic processing pipelines.
For AncientMetagenomeDir:
For AMDirT
Contact person(s): James Fellows Yates and Maxime Borry
Ancient Metagenomics Labs
The SPAAM community also curate a list of known labs working in ancient metagenomics with an aim to help improve collaboration by making labs around the world more visible.
The list of labs can be found here
Contact person(s): James Fellows Yates
MINAS MIxS Checklist
Metadata about samples and data is crucial for the implementation of FAIR principles. Providing rich metadata also helps researchers to improve the quality of their work, allowing further insights into their and previously published data.
An issue for the existing MIxS checklists, is they are designed for modern sequence data, and are missing critical metadata fields, and/or include fields that have definitions that do not fit well in an ancient context.
To facilitate improved metadata reporting in paleogenomics, the SPAAM community are establishing a working group to develop a MIxS extension checklist designed specifically for ancient metagenomics, as well as collaborating with a working group in ancient human population genetics to develop a more general checklist for ancient DNA, provisionally called the ‘MInAS’ checklist (Minimum INformation about Ancient Sequences’).
The MInAS website can be found here. Please join the SPAAM Slack workspace and #metadata-standards channel to join the working group.
Contact person(s): James Fellows Yates and Antonio Fernandez-Guerra
SPAAM Summer Schools
To help widely disseminate knowledge and expertise in ancient metagenomics, groups in the SPAAM community offer various training workshops.
These will occur on either on a regular basis or as on-off events, so generally please keep an eye on the events page, as well as the various social media channels.
We will list regular events here, as well as those that make their training material availble online for self learning:
- Annually
- Website: https://spaam-community.github.io/wss-summer-school/
- Supported by: Werner Siemens-Stiftung, Hans Knöll Institute, MHAAM, MPI-EVA, JSMC
Contact person(s): James Fellows Yates and Christina Warinner
SPAAM Blog
The SPAAM community hosts a blog that hosts posts from members on a wide-range of ancient metagenomics topics, such as short deep-dive into technical methods, or summarising discussions of questions posted in the slack channel. You can request or post posts on the #spaam-blog channel on the SPAAM slack workspace.
You can see all blog posts here.
Contact person(s): Ele Green and Shreya Ramachandran
SPAAMtisch
The community has a monthly online get-together on the SPAAM gather.town space for those who want to discuss some topics of interest chosen by the community, and in an informal and stress-free way! No knowledge or preparation required!
More information and topics can be found on the #spaamtisch channel on the SPAAM slack workspace.
Contact person(s): Maria Lopopolo
Introduction to Ancient Metagenomics Textbook
In addition to providing direct teaching of the summer school, the SPAAM community has decided to also further expand our educational reach by converting the Introduction to Ancient Metagenomics summer school teaching material into a textbook, that can be used by any researcher from around the world to go through the summer school material in their own time.
The draft text book can be found at http://spaam-community.org/intro-to-ancient-metagenomics-book/
Contact person(s): James Fellows Yates and Christina Warinner
Little Book of Smiley Plots Book
A key authentication method in ancient DNA is to show the presence of elevated C to T deamination patterns (and the complementary G to A) at the end of DNA molecules - known as damage patterns - originally reported by (Briggs et al. 2007). These patterns can be plotted in what have been colloquially known as ’Smiley Plots. However, there can be a wide range of smiley plots, some which show valid ancient DNA, and others that do not - either due to not actually having true ancient DNA but also from laboratory and/or bioinformatic artifacts.
This book aims to act as a light hearted reference guide to interpreting ancient DNA damage plots, providing a wide range community-submitted example ‘smiley plots’, with descriptions of what the describe and what can cause them. As an added bit of fun, each type of ‘smiley plot’ comes with a artistic interpretation of the line shape contributed by members of the ancient DNA community.
This book can be found at: https://spaam-community.org/little-book-of-smiley-plots/
Contact person(s): James Fellows Yates and Aida Andrades Valtueña
