Docs: Downstream Processing Tutorial

[Adamtaranto]

Standard TIRmite tutorial

Prerequisite tutorial: Document basic detection and annotation workflow for one ITR (F,R) and one asymmetrical (F,F) element example.

• Build HMMs from seed.
• Search with BLAST and HMMER ensemble method
• Run pairing module and extract candidate elements
• Validate model boundaries with empty sites database

Downstream Processing

Clustering

• Cluster predicted elements with mmseqs2
• Cluster predicted elements based on mer distance with sourmash (jaccard similarity)
• Script to update element GFF3 with cluster IDs

Consensus

• Generate within cluster MSA with mafft
• Test for RIP in fungal sequences wit derip2
• Generate consensus sequence or HMM as reference for use with repeatmasker

Visualisation

• Element length distribution
• Cluster abundance
• Ribbon plot aligning different cluster consensus sequences
• Flexidot dotplot array for comparing cluster representatives

Element annotation and classification

Need to look into the conserved domain sets that other TE classification tools use.

• Annotate with TE conserved domains
• Annotate with CDD database
• Annotate with full PFAM
• tsplit for annotation of terminal repeats