The pipeline indicated below is to be used in identifying antimicrobial resistance genes using long reads sequenced from Oxford nanopore. The sequenced samples were previously identified as being resistant to commonly used antibiotics using antibiotics susceptibility tests (ASTs).
The pipeline was run using nextflow. The raw reads were basecalled and demultiplexed using Guppy.
The quality of the nanopore reads were first assessed using FastQC.
Fastqc - Check the quality of the reads.
Porechop - removal of adapters.
Filtlong - Filtering of reads.
Flye - de novo assembly of the reads.
Quast - Checking the quality of the assembled genome.
Bwa - indexing the reads and mapping reads to assembled genome.
racon + medaka - polishing of the reads.
Abricate - identify AMR genes and plasmid