Shigella virus 2019SD1 infecting shigella dysenteriae type 1
DNA sample of 2019SD1 phage was end-repaired using NEBnext ultra II end repair kit (New England Biolabs, MA, USA) and cleaned up with 1x AmPure beads (Beckmann Coulter, USA). Native barcode ligation was performed with NEB blunt/ TA ligase (New England Biolabs, MA, USA) using NBD103 (ONT) and cleaned with 1x AmPure beads. Qubit quantified barcode ligated DNA samples were then pooled at equimolar concentration to attain 500 ng pooled sample. Adapter ligation (BAM) was performed for 15 min using NEBnext Quick Ligation Module (New England Biolabs, MA, USA). Library mix was cleaned up using 0.4X AmPure beads (Beckmann Coulter, USA) and finally sequencing library was eluted in 15 l of elution buffer and used for nanopore sequencing. Sequencing was performed on GridION X5 (Oxford Nanopore Technologies, Oxford, UK) using SpotON flow cell (R9.4) in a 48hr sequencing protocol on MinKNOW 2.1 v18.05.5. Nanopore raw reads (fast5 format) were basecalled (fastq5 format) and demultiplexed using Albacore v2.3.1. All the raw data were subjected for basecalling and demultiplexing using Albacore. Basecalled reads from each sample were error corrected and assembled using Canu assembler v1.8