DOI: 10.5061/dryad.c59zw3rm7
title: HG002 DNA (PacBio and ONT) and UHRR RNA (ONT) base modification data for minimod

description: 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.
description: # 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](https://github.com/lh3/minimap2) (version 2.28) with the
 following commands: ``` # HG002 DNA on ONT PromethION samtools fastq
 -TMM,ML hg002_prom_PGXXSX240041_unaligned.bam | minimap2 -ax map-ont -Y -y
 --secondary=no hg38noAlt.fa - | samtools sort - -o
 hg002_prom_PGXXSX240041_aligned.bam # HG002 DNA on PacBio Revio samtools
 fastq -TMM,ML hg002_revio_RGBX240039_unaligned.bam | minimap2 -ax map-hifi
 -y -Y hg38noAlt.fa --secondary=no - | samtools sort - -o
 hg002_revio_RGBX240039_aligned.bam # UHRR RNA on ONT PromethION samtools
 fastq -TMM,ML uhrr_prom_PNXRXX240011_unaligned.bam | minimap2 -ax map-ont
 -Y -y --secondary=no -uf gencode.v40.transcripts.fa - | samtools sort -o
 uhrr_prom_PNXRXX240011_aligned.bam ``` For nanopore data, the raw nanopore
 signal data available through the below ENA accessions (see Access
 information) were basecalled using the following commands to generate the
 unaligned BAM files: ``` # DNA buttery-eel -g /dorado/bin --port 5000
 --use_tcp --device cuda:all --call_mods --config
 dna_r10.4.1_e8.2_400bps_5khz_modbases_5hmc_5mc_cg_hac.cfg -i reads.blow5
 -o unaligned.sam && samtools view unaligned.sam -o unaligned.bam #
 RNA slow5-dorado basecaller rna004_130bps_sup@v5.0.0 -x cuda:all
 reads.blow5 --modified-bases m6A_DRACH &gt; unaligned.bam ``` The software
 versions used: * [buttery-eel](https://github.com/Psy-Fer/buttery-eel):
 0.6.0 * [slow5-dorado](https://github.com/hiruna72/dorado): 0.8.3 *
 [samtools](https://www.htslib.org/): 1.21 ## Code/software Any software
 that can read BAM files with MM/ML tags such as:
 [samtools](https://www.htslib.org/),
 [minimod](https://github.com/warp9seq/minimod),
 [modkit](https://github.com/nanoporetech/modkit). ## Access information
 Raw nanopore signal data in BLOW5 format is available at
 [ENA](https://www.ebi.ac.uk/) (HG002 sample:
 [ERR12997168](https://www.ebi.ac.uk/ena/browser/view/ERR12997168) and UHRR
 sample:
 [ERR12997170).](https://www.ebi.ac.uk/ena/browser/view/ERR12997170)