title: MinION sequencing of E. coli MVAST5635 strain
design: Genomic DNA fragment above 20kb were selected for barcoded library preparation. Sequencing adapters (Rapid 1D adapter, RAD) were ligated to the barcoded DNA fragments with the help of NEB Blunt/TA ligase master mix (NEB, USA). Prepared library was sequenced on Minion sequencing flow cell cell (SpotON Flow Cell Mk I R9 Version).Once the library was loaded, a standard sequencing protocol using the MinKNOW software was performed. Fast5 files were base-called and de-multiplexed using Albacore v2.0.2 (https://github.com/Albacore/albacore). Barcode and adopter sequences were trimmed from de-multiplexed sequence and corrected for any formatting errors. Then fragments above 1000 nucleotides were used for assembly on the Canu 1.76 assembler (Koren et al., 2017) platform to obtain contigs (FASTA format).