A curated list of software packages, databases, methods, and resources for transposable element research.
Transposable elements (TEs) are repetitive DNA sequences that comprise significant portions of most eukaryotic genomes (>45% human, >85% maize). They shape genome evolution, gene regulation, and contribute to genetic diversity and disease.
This will begin as a human-centered list
- Background
- TE Detection and Annotation
- TE Activity Analysis
- Population and Comparative Studies
- Experimental Methods
- Specialized Computational Approaches
- Visualization
- Quality Control and Validation
- Community
- Contributing
- License
- Acknowledgments
📚 Essential tutorials, and educational materials for understanding transposable elements.
🧬 Databases containing TE sequences, annotations, and classifications.
- DFAM: Open database of Repetitive DNA families organized around multiple sequence alignments of TE families. This is a DFAM demo by Jessica Storer.
📋 Organizing and naming transposable elements across different communities.
⚡ Tools for quickly estimating TE content without comprehensive annotation - useful for initial genome assessment.
🔍 Software for identifying novel TEs without relying on existing TE libraries - e.g. for new species or finding species-specific TEs.
🔄 Complete workflows that combine multiple tools to annotate TEs genome-wide, from initial detection to final classification.
🏷️ Software for categorizing identified TEs into families and superfamilies based on structural features and sequence similarity.
📊 Tools for analyzing TE activity in RNA sequencing data.
Methods for quantifying TE expression from RNA-seq experiments, handling multi-mapping reads and ambiguous assignments.
Specialized approaches for detecting TE expression at single-cell resolution, revealing cell-type specific TE activity.
🧪 Tools for studying TE regulation through epigenetic modifications.
Software for analyzing TE methylation patterns from bisulfite sequencing data (WGBS, RRBS).
Methods for assessing TE chromatin states using ATAC-seq, DNase-seq, and similar assays.
Tools for analyzing histone marks at TE loci from ChIP-seq data.
🔬 Software for detecting TE-derived peptides and proteins in mass spectrometry data.
🔗 Tools that integrate multiple data types to provide comprehensive views of TE activity and regulation.
👥 Tools for discovering TE insertions that vary between individuals, populations, or strains.
📈 Software for comparing TE landscapes across multiple genomes, studying TE evolution and dynamics.
🧫 Experimental techniques designed to specifically capture and sequence transposable elements or their insertion sites.
🧲 Laboratory methods for enriching TE-containing DNA or RNA fragments, including immunoprecipitation and capture approaches.
📏 Specialized tools that leverage PacBio or Oxford Nanopore long reads to resolve complex TE structures and insertions.
🎨 Software for creating publication-quality figures of TE annotations, distributions, and comparative analyses.
✅ Methods and metrics for evaluating the quality, completeness, and accuracy of TE annotations.
👀 Software interfaces for expert review and refinement of automated TE predictions.
📁 Benchmark datasets, simulated data, and gold standards for testing and comparing TE detection methods.
- 💬 BioStars TE Tag - Q&A for TE analysis
- 💬 Transposons Worldwide Slack Channel - Active research community
- Transposable elements labs: a list of labs studying TEs by the Mobile DNA journal
- 🎤 [International Conference on Transposable Elements](link needed) - e.g. Biennial conference
- 🎤 [Mobile DNA Conference](link needed) - e.g. Regional meetings
- 📄 Bourque et al. 2018 - Ten things you should know about transposable elements
- 📄 Wells & Feschotte 2020 - A field guide to eukaryotic transposable elements
- 📄 Goubert et al. 2022 - TE detection benchmarking
Please see our contributing guidelines. We welcome additions of:
- Well-maintained software with clear documentation
- Databases actively used by the community
- Experimental protocols
- Educational resources that have proven helpful
- Fork the repository
- Add your tool/resource with appropriate description
- Ensure you follow the format
- Submit a pull request
See here visual instructions.
This work is licensed under a Creative Commons Zero v1.0 Universal License.
Inspired by other awesome bioinformatics lists. Special thanks to all contributors and the TE research community.
Maintainers: @nixonlab, @hreypar, @mlbendall