TE Softwares

You will find below the complete list of the programs and tools I have developed or contributed during my journey in the intricacy of transposable elements.

  • dnaPipeTE (2015, latest 2017) - Detection, Assembly, Quantification, Annotation of TE from raw reads - github - pub

 

  • TypeTE (2020, co-lead with J. Thomas) - Bi-allelic genotyping of segregating (unfixed) TE - github - pub

 

  • RepeatModeler2 (2020, collaborator; lead: J. Flynn & R. Hubley) - Discovery and assembly of TE families for assembled genomes - website - pub

  • TE-Aid (2021) - Graphical exploration of TE consensus sequences for manual curation of TE libraries - github

  • consensus2genome (2017) - R script to profile putative TE copies in genome assemblies - github

For more resources, you can consult (and contribute to) the growing list TE tools available on TE-Hub