TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology and Genetics

Background:

• Transcriptome assembly and functional annotation are crucial for understanding gene expression and biological functions.
• Existing pipelines often lack flexibility for integrating diverse sequencing data (short- and long-read) or offer limited customization for non-model organisms.

Purpose of the Study:

• To develop TrAnnoScope, a flexible and comprehensive transcriptome analysis pipeline.
• To enable high-quality transcriptome assembly and functional annotation using both short-read (Illumina) and long-read (PacBio) sequencing data.

Main Methods:

• TrAnnoScope processes Illumina short-read and PacBio long-read data through a customizable workflow.
• The pipeline includes quality control, assembly, and functional annotation using established databases (SwissProt, Pfam, GO, KEGG, KOG).
• Modular design allows adaptation for various sequencing platforms and data types.

Main Results:

• Application to zebra finch data yielded a transcriptome with 99.63% alignment to the reference genome.
• 93.95% of matched protein sequences in the zebra finch proteome were captured as nearly complete.
• Functional annotation successfully matched transcripts to known protein databases and assigned relevant functional terms.

Conclusions:

• TrAnnoScope effectively integrates short and long sequencing technologies for automated transcriptome generation.
• The pipeline's modularity and user-friendliness make it a valuable tool for complex transcriptome analysis, particularly for non-model organisms.