Mastodawn

Thiseas C. Lamnidis Jul 3, 2024

Stephan Schiffels Jul 3, 2024

We’re looking for student assistants for our @poseidon Project (https://www.poseidon-adna.org). Ideally in the Leipzig area, but we would be open to discuss remote work if motivation and skills match:

https://www.eva.mpg.de/career/positions-available/job/610/Abteilung%20Archäogenetik/en/?cHash=66f99b791e858b01aebf288045d280ba

Application deadline is July 30th.

Thiseas C. Lamnidis Jun 28, 2024

🧬 A new patch release of
nf-core/eager (2.5.2) is now available!! 📢🍏
This release:
✅ Updated output documentation to include information on lane merging output.
✅ Fixed a bug stopping post-adapterremoval trimmed FastQC results from being displayed in MultiQC.
💜 Many thanks to the @nf_core community for all their support, Tessa Zeibig and Kieren J Mitchell for reporting the bugs, and to @jfy133 for helping fix things!
#nfcore #eager #patch #release #ancientDNA

Thiseas C. Lamnidis Apr 24, 2024

Stephan Schiffels Apr 24, 2024

Last week, we released our preprint on Poseidon, which seeks to make archaeogenetic data more Findable, Accessible, Interoperable and Reproducible, by defining a data package standard, software tools and public repositories and cloud infrastructure (https://www.biorxiv.org/content/10.1101/2024.04.12.589180v2) 1/9

Show thread

Thiseas C. Lamnidis Apr 15, 2024

This first post is an example of the kind of content I hope we can all fill the
@haam_community blog with, ultimately turning it into a nice resource full of didactic examples and interesting investigations!
Big thank you to @jfy133, Marina Silva, Miren Iraeta Orbegozo, @stschiff and Aida Andrades Valtueña for their valuable comments on the writeup! 🙇💜

Thiseas C. Lamnidis Apr 15, 2024

📢Our first blog for the
@haam_community website:
Missing data and PCA: How little is too little?
https://haam-community.github.io/blog/2024/04/15/blog/
We all have a “feeling” of how much we trust the position of our low-coverage samples in PCA space, but does the data agree with our gut? 🤔
#HAAMcommunity

Missing data and PCA · HAAM Community

Thiseas C. Lamnidis Mar 21, 2024

nf-core Mar 21, 2024

And just like that, the March 2024 online / distributed @nf_core #hackathon is complete! 🎉

HUGE thank you to everyone who participated, helped, organised and was involved 🤗

We leave you with a song by the talented @TCLamnidis and @jfy133 - the perfect wrap up! 🎵👼🏻🍏🧦

Thiseas C. Lamnidis Feb 21, 2024

🧬 Patch release of nf-core/eager (2.5.1) is out!! 🍏
✅ adds the option to use unsorted anno files in bedtools coverage.
✅ Fixes issue when vcf2genome was run on many samples with --vcf2genome_outfile provided
✅ Fixes a VERY niche issue where input BAMs named `*.unmapped.bam` were emptied out when ran through bam_filtering. Now error is thrown.
✅ Some statistics in the MultiQC report moved to sample level from their own row
Big ❤️ to @nf_core, Ido Bar, Meriam van Os and Pablo Carrion.🍏
#nf_core

Thiseas C. Lamnidis Feb 8, 2024

Poseidon Framework Feb 8, 2024

Last week @ClemensSchmid gave a short introduction to Poseidon for the #aDNA Archaeo- and Paleogenetics Group at the Institute for Archaeological Sciences in Tübingen.

He prepared it in the form of a website with multiple consecutive mini-tutorials embedded in a fun little mystery story ⛰️ :
https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024

If you're curious about Poseidon but don't want to read through the more technical documentation on the website, then this might be a good starting point.

twitter	https://twitter.com/TCLamnidis
WEBSITE (MPI)	https://www.eva.mpg.de/archaeogenetics/staff/thiseas-christos-lamnidis/
GITHUB	https://github.com/TCLamnidis

Missing data and PCA · HAAM Community

Poseidon introduction for Tübingen University, February 2024 - A short introduction to the Poseidon genotype data management framework