Shallow whole genome sequencing of cell free DNA with Oxford Nanopore Technology shows promise for the detection of cell type and cancer-specific methylation changes. NBThighlight
: Table S1. Barcoded libraries were created using the NBD-EXP104 and SQK-LSK109 kits as described for the ISPRO samples. They were sequenced on a single flow cell, using standard MinKNOW runtime control without modification.Base calling was done using “high-accuracy real-time” mode during the run using MinKNOW distribution v.18 for run S1, and v.19.06.9 Guppy version 3.0.6+9999d81 for the others.
These are the primary files used for all methylation analysis, described in more detail below, and are available from GEO GSE185307 and at Zenodo DOI: 10.5281/zenodo.6642503.We used DeepSignal Version 0.1.8 , with model “model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt,” which was downloaded from the DeepSignal Google Drive .
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