Install via conda:
conda install -c conda-forge -c bioconda -c toby_baril_bio earlgrey-partea

Docs & source: github.com/TobyBaril/EarlGreyParTEA

🖥️ New: SLURM cluster support! Pass `--slurm --slurm-partition <queue>` and ParTEA submits each rule as its own sbatch job. Per-rule CPUs, memory & wall-time are all pre-configured.

🌳 New: BUSCO phylogenomics! `run_busco_phylo: true `runs BUSCO, aligns single-copy orthologs, builds a supermatrix & infers a species tree with FastTree — then reorders your TE plots by the tree. This also includes QC plots to assess the impact of completeness on TE content.

🔀 New: shared/unique TE content analysis! Enable `run_shared_unique: true` to get stacked bar charts showing which TE families are core, partially shared, or unique across your genomes. Works in full & annotate modes.

🎉 EarlGrey ParTEA v0.1.6 is here! Huge thanks to everyone who's tried the pipeline and shared feedback — your suggestions directly shaped these new features. 🍵

#TEworldwide #transposableelements #bioinformatics #genomics

⚠️ Early release: ready for testing & feedback!
Try it on your genome collection and let us know what works (or breaks!). Especially keen to hear from anyone with diverse or large genome sets.
📝 Manuscript in prep
💬 Issues/suggestions welcome on GitHub or DM
#Bioinformatics #Genomics

ParTEA handles the hard parts of multi-genome TE annotation:
🔄 Parallel library construction across all genomes
🏷️ Optional clustering → one consistent TE library annotates every genome
📈 Saturation curves: see how TE diversity grows as you add genomes
⚡️ One config, one command
From 2 to 20+ genomes!

🎉🧬 Multiple genomes/pangenome? Time for a parTEA! 🧬 ☕️

Tired of annotating TEs one genome at a time? Same. So we organised a parTEA!

Introducing EarlGrey ParTEA v0.1.3 — consistent TE annotation across all your genomes, in parallel, with one command: github.com/TobyBaril/Ea...

#TEworldwide #TEsky

We are looking for a Postdoc to join our lab at @oxfordbiochemistry.bsky.social. This is a dry-lab focused post on the computational analysis of long read single-cell sequencing data to understand the role of transposable elements (TEs) in early development. my.corehr.com/pls/uoxrecru... #TEsky

Had a great chat with Sophie about this work back in Heidelberg, excited to dive into this preprint!

#TEsky #TEworldwide

#TEsky a short paper from @mbonar.bsky.social , myself and others on our reannotation of TEs in the Octopus vulgaris genome. More work to come using genome ecology to analyze TEs in this species bsky.app/profile/bior...

#TEworldwide #TEsky

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r

Need to annotate transposons in fungal genomes? 🧬
Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg...
Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social!

w/ @danielcroll.bsky.social

EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis - BMC Genomics BMC Genomics - Transposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator...

#TEsky EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis doi.org/10.1186/s128...

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics

#TEworldwide #TEsky

www.sciencedirect.com/science/arti...

👏 Congratulations Toby for this Current Biology dispatch!
🎨 Happy to see my watercolours in it to illustrate this so-cool topic!

#illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide

I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at

The influence of transposable elements on animal colouration Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transp…

Relatively specific in terms of function, but a nice review of functions in animal coloration!

www.sciencedirect.com/science/arti...

🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide

#TEworldwide

#TEsky #TEworldwide #Transposons #Bioinformatics #Bioconda #GenomeAnnotation #TransposableElements #Genomics #ComparativeGenomics

GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey

☕Earl Grey v7.0.0 brewed fresh☕

Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.

Happy new year to the TE folks! 🧬

github.com/TobyBaril/Ea...

Transposable elements can insert into genes, disrupting protein-coding potential. Researchers discover a mode of RNA processing, ‘SOS splicing’, that provides a quick fix @nature.com @harvardmed.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

TEs aren’t just genomic parasites, they’re also engines of genomic novelty.

Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.

With @danielcroll.bsky.social & @guidopuccetti.bsky.social

🧬 www.nature.com/articles/s41...

#TEworldwide

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...

Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5

A comparative analysis of transposable element diversity and evolution across 75 bee genomes - BMC Genomics Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...

#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...

High‐Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon‐Driven Structural Dynamics in Fungi Evolution Long terminal repeat retrotransposons (LTR-RTs) are recognised as a significant evolutionary force capable of shaping the structure and function of the genomes in eukaryotes, including animals, plant...

High-Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon-Driven Structural Dynamics in Fungi Evolution

doi.org/10.1111/1755...

#TEworldwide #TEsky

Awesome talk @orpsf.bsky.social! Excited to see what comes next!

#TEworldwide #TESky

#TEsky Evolution of Mutator transposons in the genomes of worms doi.org/10.1016/j.ge...