Oxford Nanopore MinION sequencing technology has been gaining immense importance in identification of pathogen and antimicrobial resistance, though with 10–15% error rate. Short read technologies generates high accurate genome but with multiple fragments of genome. This study proposes a novel workflow to reduce the indels resulted from MinION long read sequencing by overlaying short read sequences from IonTorrent in the clinical isolates. Best of both techniques were employed which generated highly accurate-single chromosomal microbial genomes with increase in completeness of genomes from 44.5%, 30% and 43% to 98.6%, 98.6% and 96.6% for P. aeruginosa, A. veronii and B. pertussis respectively. To the best of our knowledge, this is the first study to generate a hybrid of IonTorrent and MinION reads to obtain single chromosomal genomes. This would enable to precisely infer both structural arrangement of genes and SNP based analysis for phylogenetic information. •Novel hybrid approach revealed structural arrangement of genome at SNP level accuracy•Achieved genome completeness from ~40% (conventional approach) to ~98% (hybrid).•Chromosomal integration of non-expressive mcr-3.19 identified in A. veronii•Genome rearrangements were identified in-spite of high IS481 copies in B. pertussis.•Tn3 family transposons with novel MGEs were identified from P. aeruginosa