Dogme

Dogme automates the processing of Oxford Nanopore Technologies (ONT) RNA and DNA sequencing data through a Nextflow-based workflow that performs basecalling, alignment, modification detection, and transcript quantification.

Key Features:

• ONT Data Type Support: The pipeline supports three major types of ONT sequencing data: direct RNA (dRNA), complementary DNA (cDNA), and genomic DNA (gDNA).
• Automated Basecalling: Dogme automates reprocessing of ONT POD5 files by integrating basecalling using Dorado.
• Read Mapping: The workflow performs read mapping using minimap2.
• Modification Detection: Dogme facilitates detection of diverse RNA modifications supported by Dorado, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), inosine, pseudouridine, 2'-O-methylation (Nm), and DNA methylation.
• Transcript Quantification: The pipeline quantifies full-length transcript isoforms using LR-Kallisto for transcript quantification for dRNA and cDNA.
• Integration with modkit: Subsequent analysis steps include running modkit for modification analysis.

Scientific Applications:

• Integrative Long-read Transcriptomic and Epigenomic Analyses: Dogme enables comprehensive analyses across different library preparations, producing reproducible modification profiles and transcript expression levels across replicates.
• RNA Modification Detection: The tool detects RNA modifications including m6A, m5C, inosine, pseudouridine, and Nm from direct RNA sequencing data.
• DNA Methylation Analysis: Dogme supports detection of DNA methylation from genomic DNA sequencing data.

Methodology:

Dogme is implemented in Nextflow and automates processing steps including basecalling with Dorado, read mapping with minimap2, modification detection with modkit, and transcript quantification with LR-Kallisto.