TAGADA

TAGADA performs transcript and gene assembly, deconvolution, and analysis to update reference genome annotations by integrating Illumina NovaSeq short reads and PacBio Iso-Seq long reads from RNA-seq projects.

Key Features:

• Annotation Enhancement: Generates updated reference annotations that incorporate newly identified transcripts, expanding the catalog of genes and transcripts for a species.
• Expression Computation: Computes expression values for existing and novel annotations to quantify transcript abundance.
• Identification of lncRNAs: Identifies long non-coding RNAs (lncRNAs) within the transcriptome data.
• Quality Control Reporting: Produces detailed quality control reports to assess the reliability and accuracy of analysis results.
• Integration of Multiple Read Types: Integrates Illumina NovaSeq short reads with PacBio Iso-Seq long reads for comprehensive transcriptome profiling.
• Reproducibility and Execution Framework: Implemented in Nextflow DSL2 and provided as a containerized environment to enable reproducible execution across computing platforms.

Scientific Applications:

• Genome annotation updating: Integrates new RNA-seq data into existing genome annotations to expand and correct gene models.
• Demonstrated project application: Applied to RNA-seq data from the GENE-SWiTCH project and reference genomes of chicken and pig, increasing the number of annotated transcripts.
• Gene model refinement and transcript diversity: Supports refinement of gene models and exploration of transcript diversity across species.

Methodology:

Accepts a genomic sequence, a reference annotation, and RNA-seq reads (Illumina NovaSeq and PacBio Iso-Seq) as inputs and processes them to enhance gene annotations, compute expression values, identify lncRNAs, and generate quality control reports; implemented in Nextflow DSL2 and executed in a containerized environment.