TransposonDB - database of transposable elements

This record contains some of the supplementary files for the TransposonUltimate package by Riehl et al. Please see https://github.com/DerKevinRiehl/TransposonUltimate for code.

Folder "Assemblies" contains the 40 polished scaffolded assemblies of 20 C. elegans wild isolates, created by Cristian Riccio. 20 assemblies were scaffolded using the VC2010 reference. 20 assemblies were scaffolded using the CB4856 reference. We release the data under the usual Fort Lauderdale/Bermuda agreements. We will publish a paper about these genomes ourselves but we allow you to mine the dataset for a gene-specific analysis. Please contact us if you would like to publish anything using these data before our genome publication.
Folder "Classification" contains the TransposonDB in FASTA file format, that was introduced in the context of the transposon classification module "RFSB".
Folder "Annotation" contains the transposon annotations of the C. elegans and O. Sativa ssp. Japonica genomes, that were generated using the "reasonaTE" transposon annotation module.
Folder "Detection" contains the detected transposition events in the context of the transposon detection module "deTEct". All 20 wild isolates assemblies of C. elegans were used as probe genomes, and compared to the two reference genomes "VC2010" and "CB4856". All combinations were investigated using PBMM2 alignments + PBSV structural variants, and NGMLR alignments + Sniffles structural variants.