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FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing
Xiaofeng Chen1,2, Yongqi Liu1,2, Kaiwen Lv1,2
1Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China.
Bioinformatics Advances
|July 31, 2023
Summary
FASTdRNA is a novel workflow for efficient direct RNA sequencing (dRNA-seq) data analysis. It optimizes basecalling, mapping, and downstream analyses like RNA modification prediction, improving research capabilities.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Direct RNA sequencing (dRNA-seq) with Oxford Nanopore Technology (ONT) offers precise transcript mapping and preserves base-level information.
- Traditional dRNA-seq analysis faces challenges with software compatibility and efficiency due to rapid technological advancements.
Purpose of the Study:
- To develop an efficient and comprehensive workflow for dRNA-seq data analysis.
- To address limitations in existing dRNA-seq software, enhancing analytical capabilities.
Main Methods:
- Developed FASTdRNA, a Snakemake-based workflow with distinct preprocessing and analysis modules.
- Preprocessing module (dRNAmain) includes basecalling, mapping, and transcript counting.
- Analysis module supports poly(A) length estimation, RNA modification prediction, and alternative splicing assessment.
Main Results:
- FASTdRNA demonstrates superior performance compared to existing methods in comparative experiments.
- The workflow efficiently handles dRNA-seq data, enabling local or cloud execution.
- Successfully integrated essential downstream analyses for comprehensive dRNA-seq data interpretation.
Conclusions:
- FASTdRNA significantly enhances dRNA-seq data analysis pipelines.
- The workflow optimizes existing processes and expands the scope of RNA analysis.
- Provides a robust and efficient solution for researchers utilizing dRNA-seq technology.
