Interspersed repeats are present in virtually all genomes and make up the bulk of most eukaryotic genomes; they are generally the remnants of copies of transposable elements (TEs) both old and young. The ubiquitous presence of TEs is common knowledge, due to both the challenges they pose in genome sequence assembly and analysis and theirclear role as an evolutionary force, through gene regulation, formation of novel genes, and global genomic rearrangements. The role of TEs has been extensively studied in the context of their contribution to genetic biodiversity, disease emergence, cancer progression, plant and animal breeding, and even gene therapy. Identification and analysis of TEs have therefore become an intrinsic part of any genome-wide approach. However, in-depth TE detection and analysis is laborious, and largely requires significant expertise in TE biology. There exists a plethora of overlapping (but independently maintained) methods, often only communicated from mentor to mentee; this, combined with the manual nature of analysis, presents a challenge to reproducibility and reusability. Furthermore, the computational resources required to perform these analyses are substantial, in terms of both computational burden and the complexity/dependency landscape of interacting software tools.

This 3-day workshop seeks to facilitate access to the scientific knowledge and understanding of these enigmatic sequences while simultaneously lowering the technical and computational barriers by providing explicit examples using the most used programs available for TE analysis. The target audience is any researcher who is interested in understanding more about the importance of curating repetitive sequences. Although all levels are welcome, it is encouraged for users to have basic coding knowledge of perl, python and bash and high comfort level navigating directories using the command line. Such knowledge is crucial when running the programs necessary to generate output for subsequent filtering and analysis.

This workshop will give an overview of the best practices for assembling repetitive parts of the genome, how to check assemblies and then curate and annotate the genome for TEs. Our understanding of repetitive parts of the genome is increasing, as we find an important role for these challenging to assemble parts of the genome. This workshop will outline ways to streamline and improve assembly and interpretation of TEs and repetitive parts of the genome to ensure we are making the best interpretations of the repetitive parts of the genome. The workshop will also include a background seminar from Rachel O’Neill on repetitive regions of genomes and what they can tell us about genome evolution and discussion on genome assembly approaches, successes and pitfalls.
 

Workshop outline

Each section will incorporate best practices in reporting, tracking, project set-up, and data limitations and interpretations.

Background

• (Introduction) Genome assemblies: the impact of repeat annotations in understanding genome structure, function and biology
• Current databases
• Satellites and other non-TE repeats
• Transposable elements
  • Brief history
  • Categories

Pipelines

• EDTA, Earl Grey, RepeatModeler2
• De novo satellite annotation

Collecting more copies/extension

• Non-competitive vs. competitive: blast, extract, extend (BEE) method vs. RepeatMasker/RAM

Visualization

• HTML MSA
  • Shapes reflect TE type
• Dot plots
• NCBI blastx output (for autonomous elements)

Redundancy

• Pairwise comparison against known models