TranscriptomeReconstructoR

TranscriptomeReconstructoR reconstructs transcriptomes by integrating full-length RNA-seq, high-throughput 5' and 3' tag sequencing, and optional nascent RNA-seq to generate accurate gene and transcript models anchored to a reference genomic DNA sequence.

Key Features:

• Integration of Complementary Datasets: Integrates full-length RNA-seq to detect complex splicing patterns, high-throughput 5' and 3' tag sequencing to precisely delineate gene borders, and optional nascent RNA-seq to identify transient transcripts.
• De Novo Annotation: Reconstructs transcriptomes de novo using only the reference genomic DNA sequence without requiring pre-existing transcriptome annotations.
• Bioconductor Integration: Integrates with Bioconductor packages to enable downstream analysis within existing bioinformatics workflows.

Scientific Applications:

• Annotation improvement: Improves transcriptome annotation accuracy and comprehensiveness by combining complementary experimental datasets.
• Arabidopsis thaliana transcriptome annotation: Applied to wild type Arabidopsis thaliana seedlings and produced annotations that outperformed TAIR10 and Araport11, identifying thousands of transient transcripts previously unannotated.

Methodology:

Implements a data-driven automated annotation pipeline that constructs gene and transcript models from integrated sequencing datasets.