HG002 DNA (PacBio and ONT) and UHRR RNA (ONT) base modification data for minimod

Recent advances in third-generation sequencing technologies have enabled the detection of various DNA and RNA base modifications in addition to standard nucleotide sequences. Both major vendors in this space—Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio)—now include base modification information in their sequencing outputs using MM/ML tags embedded in unaligned BAM files. Each vendor also provides dedicated tools for extracting and analysing these tags, such as ONT’s modkit and PacBio’s pb-cpg-tools.
This work presents Minimod, a new vendor-agnostic tool designed to extract and analyse any type of base modification from sequencing data generated by any platform that supports MM/ML tags. Minimod is a free, open-source application written in C and is available in GitHub and Zenodo (see related works). This dataset provides the supporting data used to evaluate Minimod’s performance., , # Data for minimod

Dataset DOI: [10.5061/dryad.c59zw3rm7](10.5061/dryad.c59zw3rm7)

## Description of the data and file structure

The dataset includes three samples:

* HG002 DNA sequenced on an ONT PromethION using R10.4.1 chemistry
* HG002 DNA sequenced on a PacBio Revio
* UHRR RNA sequenced on an ONT PromethION using RNA004 chemistry

### Files and variables

Both unaligned and aligned BAM files containing MM/ML tags are available for each sample as follows:

* HG002 DNA sequenced on an ONT PromethION
* `hg002_prom_PGXXSX240041_unaligned.bam` - also contains move table tags
* `hg002_prom_PGXXSX240041_aligned.bam`
* HG002 DNA sequenced on an PacBio Revio
* `hg002_revio_RGBX240039_unaligned.bam` - also contains kinetic data tags
* `hg002_revio_RGBX240039_aligned.bam`
* UHRR RNA sequenced on an ONT PromethION
* `uhrr_prom_PNXRXX240011_unaligned.bam`
* `uhrr_prom_PNXRXX240011_aligned.bam`

Aligned BAM files were generated by aligning the unaligned BAM files using [minimap2]...,