2026-10-12T17:31:03Z https://www.scidb.cn/oai

10.57760/sciencedb.27334 2025-09-12T14:31:29Z

2025-09-12 HG002-HG004 R9 methylation basecalled data doi:10.57760/sciencedb.27334 en Raw FAST5 files were downloaded from human pangenome reference consortium s3://human-pangenomics/NHGRI_UCSC_panel/.Basecalling was performed using Guppy v4.2.2 or v6.3.8 with the command: “guppy_basecaller --bam out -r -i ${fast5_data} -s ${output_directory} -x cuda:0,1 -c ${config.cfg}”. The resulting BAM files were merged using samtools with command “samtools merge -l ${bam_list.txt} -o ${merged.bam}”. The merged BAM file was aligned to the GRCh38 reference genome (GenBank assembly ID GCA_000001405.15) using dorado v0.9.5 (https://github.com/nanoporetech/dorado) with command “dorado align -t 80 --mm2-opts "-x map-ont" ${reference.fa} > ${output.bam}”, followed by sorting and indexing with Samtools.It should be noted that for datasets basecalled with Guppy v4.2.2 contained “Mm” and “Ml” tags instead of the standard “MM” and “ML” were presented in output BAM file. These BAM files were therefore updated using the command “modkit update-tags ${input.bam} ${output.bam}” before methylation calling. nanopore; bam; methylation Jun Mencius PUBLIC https://creativecommons.org/licenses/by-nc-nd/4.0/ dataset Science Data Bank