Source 1primary paper2026MED
Toolkit/Dogme
Dogme
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
we developed Dogme to automate basecalling, alignment, modification detection, and transcript quantification. Dogme automates the reprocessing of ONT POD5 files
Usefulness & Problems
No literature-backed usefulness or problem-fit explainer has been materialized for this record yet.
Published Workflows
Objective: Provide a reproducible and standardized workflow for reprocessing Oxford Nanopore POD5 data to detect RNA and DNA modifications and quantify transcripts.
Why it works: The workflow integrates basecalling with Dorado, mapping with minimap2, modification analysis with modkit, and LR-Kallisto transcript quantification into one automated reprocessing pipeline.
direct detection of RNA and DNA modifications from unamplified nucleic acidsbasecallingread mappingmodification detectiontranscript quantificationworkflow automation
Stages
- 1.Basecalling(broad_screen)
Basecalling is the first automated processing stage named in the abstract and is required before alignment and downstream modification analysis.
Selection: Convert ONT POD5 signal data into basecalled reads using Dorado.
- 2.Read mapping(secondary_characterization)
Mapped reads provide positional context for subsequent modification analysis and transcript quantification.
Selection: Map reads using minimap2.
- 3.Modification detection(functional_characterization)
This stage produces the modification calls that are a central output of the workflow.
Selection: Run downstream analysis steps such as modkit to extract modification information from nanopore data.
- 4.Transcript quantification(functional_characterization)
The workflow concurrently quantifies transcripts alongside modification detection for integrative transcriptomic and epigenomic analysis.
Selection: Quantify full-length transcript isoforms with LR-Kallisto for dRNA and cDNA.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Target processes
No target processes tagged yet.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Observations
successMammalian Cell Lineapplication demomouseC2C12 myoblast
direct RNA sequencing
Inferred from claim c4 during normalization. Applied to three mouse C2C12 myoblast direct RNA sequencing replicates, Dogme detected multiple RNA modification site classes and produced reproducible modification profiles and transcript expression levels across replicates. Derived from claim c4.
Source:
biological replicates3inosine sites detected8829m5C sites detected43476m6A sites detected96603Nm sites detected30320pseudouridine sites detected10055
Supporting Sources
Ranked Claims
Applied to three mouse C2C12 myoblast direct RNA sequencing replicates, Dogme detected multiple RNA modification site classes and produced reproducible modification profiles and transcript expression levels across replicates.
biological replicates 3inosine sites detected 8829m5C sites detected 43476m6A sites detected 96603Nm sites detected 30320pseudouridine sites detected 10055
Dogme automates ONT POD5 reprocessing including basecalling, alignment, modification detection, and transcript quantification.
Dogme facilitates detection of m6A, m5C, inosine, pseudouridine, 2'-O-methylation, and DNA methylation, and quantifies full-length transcript isoforms with LR-Kallisto for dRNA and cDNA.
Dogme supports direct RNA, cDNA, and genomic DNA sequencing data.
Approval Evidence
1 source4 linked approval claimsfirst-pass slug dogme
we developed Dogme to automate basecalling, alignment, modification detection, and transcript quantification. Dogme automates the reprocessing of ONT POD5 files
Source:
application resultsupports
Applied to three mouse C2C12 myoblast direct RNA sequencing replicates, Dogme detected multiple RNA modification site classes and produced reproducible modification profiles and transcript expression levels across replicates.
Source:
tool capabilitysupports
Dogme automates ONT POD5 reprocessing including basecalling, alignment, modification detection, and transcript quantification.
Source:
tool capabilitysupports
Dogme facilitates detection of m6A, m5C, inosine, pseudouridine, 2'-O-methylation, and DNA methylation, and quantifies full-length transcript isoforms with LR-Kallisto for dRNA and cDNA.
Source:
tool scopesupports
Dogme supports direct RNA, cDNA, and genomic DNA sequencing data.
Source:
Comparisons
No literature-backed comparison notes have been materialized for this record yet.
Ranked Citations
- 1.