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Updated: Jun 3, 2025

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

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Published on: March 5, 2022

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

Aysevil Pektas¹, Frank Panitz^1,2, Bo Thomsen¹

¹Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.

|January 8, 2025

Summary

TrAnnoScope integrates short and long sequencing data for robust transcriptome assembly and functional annotation, especially for non-model organisms. This pipeline generates high-quality full-length transcripts with comprehensive annotation, simplifying complex genomic analyses.

Keywords:

Iso-Seq RNA-Seq functional annotation high-performance computing (HPC)long-read sequencing reproducible pipeline snakemake transcriptome analysis

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Last Updated: Jun 3, 2025

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

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.