Thanks! ParTEA is built on top of EarlGrey, built to run and curate output from RepeatModeler and various other tools for eukaryotic TE detection.

I am sure one could re-implement the software to tune it for bacterial selfish element detection but we have done no testing in this direction.

💡 #KnowledgeHighlight | Tutorial: Repeat Annotation using RepeatModeler and RepeatMasker
darencard.net/blog/2022-07...

Explore open-access training materials in the ERGA #KnowledgeHub ➡️ knowledge.erga-biodiversity.eu
#repeats #genomics #annotation #repeatmodeler #repeatmasker #bioinformatics

A new RepeatModeler release is available. It adds compatibility with RepeatMasker 4.2.4 and the Dfam 4.0 FamDB format. TETools containers have also been updated with the latest RepeatMasker, RepeatModeler, and FamDB releases. See repeatmasker.org for details

Multiple Software Updates - RepeatMasker 4.2.0, RepeatModeler 2.0.7, and the newly released RepeatAfterMe tool. See www.repeatmasker.org for details.

RepeatModeler 2.0.6, RepeatScout 1.0.7, and Updated Dfam 3.8 FamDB Files. Improvements to coordinate reporting, and RepeatScout seed alignment generation. Fixes for primate annotation with Dfam 3.8. See www.repeatmasker.org or details.

RepeatMasker 4.1.7 Released. Several important updates and fixes are included in this release, especially for RepeatModeler/TETools users. Please see www.repeatmasker.org for more details.

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #reproducibility

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #RRID

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #RRID

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience

Authors published a paper in Biorxiv, they used RepeatModeler in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience

funannotate.readthedocs.io/en/latest/pr...
Thanks! I tried it with Histoplasma and the tantan algorithm included in Funannotate. That is a very light-touch masker, and hardmasking gave me the same SNP tree.

Need to get RepeatMasker/RepeatModeler to work to be sure, but may not make a difference.

EarlGrey ParTEA v0.2.0 is out!

Pangenome TE annotation across multiple genomes just got a major upgrade — now fully compatible with RepeatMasker 4.2.4, RepeatModeler 2.0.9, RMBlast 2.17, and Dfam 4.0 / FamDB 3.0.0 🧬

🔗 github.com/TobyBaril/EarlGreyParTEA

#TEworldwide #TEsky #genomics #transposons

I tried that a while ago, but this never really worked for us. There is a way to catch overabundant HSPs in a first round, mask them and then align, but for us this is the last resort. RepeatModeler+Masker seems to work generally well (when done for ref and query).