title: Illuminas raw read
design: The Actinomyces oris MG-1 strain was revived from a 80C glycerol stock by streaking onto HIB agar plates, followed by incubation at 37C in a 5% CO atmosphere. Genomic DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit (Zymo Research) according to the manufacturers instructions. DNA concentration was quantified with a Qubit 4 fluorometer (Thermo Fisher Scientific).Whole-genome sequencing was performed by SeqCenter (Pittsburgh, PA) using both Illumina and Oxford Nanopore Technologies (ONT) platforms. For Illumina sequencing, libraries were prepared using the Illumina DNA Prep Kit (tagmentation- and PCR-based) with custom 10 bp unique dual indices (IDT), targeting an average insert size of 280 bp. No additional fragmentation or size selection was performed. Sequencing was carried out on an Illumina NovaSeq X Plus system, generating 2151 bp paired-end reads in multiplexed shared-flow-cell runs. Demultiplexing, quality filtering, and adapter trimming were conducted using bcl-convert (v4.2.4).ONT libraries were prepared using the Ligation Sequencing Kit (SQK-NBD114.96) in combination with the NEBNext Companion Module (E7180L), following the manufacturers protocol without additional DNA fragmentation or size selection. Sequencing was performed on GridION or PromethION platforms using R10.4.1 flow cells in 400 bps mode, with a minimum read length of 200 bp. Adaptive sampling was not enabled. Basecalling was done using Dorado (v0.5.3) with both super-accurate (sup) and 5mC/5hmC models. Demultiplexing was performed with Dorado under SQK-NBD114.96 kit settings, and FASTQ files were generated from BAM files using samtools fastq (v1.20).