[question]: mergebam and strand split logic

[tamuanand]

Hi @alimortazavi-uci

I am new to DRS and ONT in general.

Thanks a lot for your work and the preprint here - I learnt a lot. Keep up the great work.

I had a question pertaining to below section from the preprint and the related code here:

• https://github.com/mortazavilab/dogme/blob/main/nanoporeModule.nf#L443-#L445
• https://github.com/mortazavilab/dogme/blob/main/nanoporeModule.nf#L84-#L93

The default Dogme workflow ([Fig. 1A](https://www.biorxiv.org/content/10.1101/2025.06.04.657941v2.full#F1))
starts by downloading the latest Dorado models, then proceeds with base-calling individual POD5 files 
using Dorado in parallel to produce one BAM file per POD5, which are then 
merged into a single unmapped BAM file stored in the bams folder.

The question: I am very curious to understand your login on why you chose to output 1 bam per pod5 and then merge them. I ask so because dorado can basecall from a folder of pod5s and even do so recursively to output a unmaoped bam. I am sure you would have had some underlying logic for the above and would like to know the same.

The other question I had was on your strategy of separating + and - strands before modkit, then use nextflow concat to obtain a combinedStrand which becomes the input to modkitTask.

• https://github.com/mortazavilab/dogme/blob/main/nanoporeModule.nf#L368-#L372
• https://github.com/mortazavilab/dogme/blob/main/nanoporeModule.nf#L178-#L186

# will automatically create separate bedGraph files for the positive and negative strand
modkit pileup path/to/reads.bam output/directory/path --bedgraph 

My question: modkit pileup with the --bedgraph command will automatically separate data into separate strands. Hence, I am very curious to understand your logic of separating by strand, concat with nextflow and then calling modkit - I want to learn from you on this.

Thanks in advance for your time and help.