title: Raw reads: Tsu-0_met1_03 DNA kinetics
design: The plant material from rosettes of a single 35-days-old individual was finely ground with mortar and pestle in liquid nitrogen, and high-molecular-weight (HMW) DNA extraction was carried out as published (Rabanal et al., 2022; doi: 10.1093/nar/gkac1115). HMW-DNA (120 ng/Î¼l) was sheared with Covaris gTUBEs (PN 520079) in a Eppendorf Centrifuge 5424 at 4,800 rpm (soft) for 3 x 1 min. Different amounts of input DNA (1480 - 5000 ng) were used for preparation of individual Tsu-0 met1 mutant HiFi SMRTbell libraries with SMRTbell Express Template Prep Kit 3.0 with 10 adapters bc1001-bc1003 and bc1008-bc1016. Prior to sequencing the final pooled libraries were size-selected on a BluePippin (SageScience) with 10 kb cutoff in a 0.75% DF Marker S1 High Pass 6-10 kb v3 gel cassette (Biozym). Final libraries were sequenced on a single SMRTcell, and resequenced on another SMRTcell multiplexed with other libraries, with the Sequel II system (Pacific Biosciences) using the Binding Kit 2.2. PacBio HiFi reads were extracted from the sequencing movies (PacBio raw format) via pbccs (--all --hifi-kinetics) and extracthifi, and further demultiplexed with lima v2.6.0 (--same --ccs --min-score 70 --min-scoring-regions 2 --min-ref-span 0.8 --peek-guess --split-bam-named) (https://github.com/PacificBiosciences/pbbioconda). We called cytosine methylation using jasmine v2.0.0, mapped them to the Tsu-0 reference genome using the align option of pbmm2 v1.10.0, and generated site methylation probabilities with the aligned_bam_to_cpg_scores tool v2.3.2 from pb-CpG-tools suite (https://github.com/PacificBiosciences/pb-CpG-tools) using the provided model.