TrAnnoScope

TrAnnoScope integrates Illumina short-read and PacBio long-read sequencing data to generate high-quality, full-length transcripts with broad functional annotation.

Key Features:

• Modular workflow: The pipeline provides a customizable, modular Snakemake workflow adaptable for other sequencing platforms or data types.
• Full-length transcript generation: Produces high-quality, full-length transcripts from combined short-read and long-read data.
• Functional annotation: Assigns functional annotations using SwissProt, Pfam, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG) databases.
• Quality control integration: Encompasses steps from quality control through functional annotation.
• Non-model organism compatibility: Supports transcriptome analysis for organisms without well-established reference genomes.

Scientific Applications:

• Transcriptome assembly: Generates transcriptomes from RNA-Seq and Iso-Seq data across multiple tissues.
• Proteome completeness assessment: Captures nearly complete protein sequences as demonstrated by 93.95% matched protein sequences in zebra finch proteome analysis.
• Functional genomics: Assigns known protein database matches and relevant functional terms to transcript sets.
• Comparative transcriptomics: Enables cross-tissue analysis as demonstrated with brain, ovary, and testis tissues in zebra finch.

Methodology:

The pipeline employs a Snakemake-based modular workflow with steps from quality control to functional annotation, using established databases including SwissProt, Pfam, Gene Ontology, KEGG, and KOG.