title: Illumina sequencing of E. coli MVAST5574 strain
design: Genomic DNA of the MVAST samples was isolated using a NucleoSpin Microbial DNA preparation kit (Machery-Nagel, Germany); Nextera XT DNA Library Preparation Kit (Illumina) was used to prepare the samples for paired-end sequencing using iSeq 100 System (Illumina) and reads longer than 150 bp were selected for further analysis. These reads were assembled with Spades assembler (SPAdes version: 3.11.1). To further improve assembly, contigs obtained with Nanopore sequencing were used as trusted contigs for hybrid assembly on Spades. Assembled contigs shorter than 300 bp were discarded using PRINSEQ v0.20.4 (Schmieder and Edwards 2011).