ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements

Transposable elements (TEs) are widespread mobile DNA sequences that shape genome structure, function, and evolution. Although automated tools exist for the de novo identification and classification of TEs, their output often requires manual refinement to generate accurate consensus sequences for individual TE families. This curation process is essential but remains time-consuming and inaccessible to many researchers, particularly those without bioinformatics expertise or access to sufficient computing resources. To address this gap, we developed ColabCuraTE, a web-based, user-friendly pipeline implemented in Google Colaboratory that enables manual curation of TEs without the need for local software installation or advanced programming skills.

ColabCuraTE includes built-in visualization tools and guides users through a streamlined workflow-from TE copy identification, alignment extension, and refinement, to consensus sequence generation and TE family analysis. We validated the pipeline using both megabase-sized and gigabase-sized genomes and found that it reliably improves the quality and completeness of TE consensus sequences compared to outputs from automated de novo TE annotation tools.

ColabCuraTE enables easier participation in TE curation by removing infrastructure and expertise requirements that typically limit participation in genomic research. It excels at the targeted curation of individual TE families but can also be used for large-scale curation efforts when deployed via a course or workshop. Its accessibility, intuitive interface, and compatibility with existing tools make it a valuable resource for both researchers and educators. ColabCuraTE enables broader participation in TE annotation efforts and supports the integration of undergraduates in genomics research.