title: Shotgun metagenomic sequencing of human stool microbiome
design: Library preparation was performed using the SQK-RBK114-24 kit in accordance with the Nanopore protocol (version RBK_9176_v114_revP_27Dec2024). The prepared libraries were loaded onto R10.4.1 flow cells and sequenced on a MinION Mk1B instrument. Data acquisition and demultiplexing were performed using MinKNOW software (v24.11.8) for 72 hours [Q-score = 10, barcode splitting = on, basecalling = super-accurate mode (r1041_e82_400bps_sup_v4.3.0), using Dorado v7.6.7]. The resulting raw reads were preprocessed to remove adaptor and barcode sequences. Host reads were then removed using the human reference genome GRCh38.p14 as a reference before any further analysis.