Library sequencing
Libraries were run on a MiniION Mk1C (ONT) using a FLO-MIN106 (R9.4.3.),
FLO-MIN111 (R10.3) or flongle FLO- FLG001 (R9.4) flow cells following
manufacturer’s protocol. The sequencing runs were initiated using
MinKNOW software (ONT), Raw data were processed with high accuracy
basecalling. Sequences with Qscore>9 were subsequently
analyzed with Guppy5 with the ‘sup’ algorithm, using a custom script in
Google Colab. All necessary steps for nDNA depletion, Cas9 targeted
sequencing, library preparation, sequencing and analyses were undertaken
using a portable setup in a home office during the Covid 19 pandemic.