Identifying bacterial resistance using plasmid sequencing

Question

[mohamed_refaat.1992]

Hi everyone,

I'm working on a project studying plasmid-borne bacterial resistance in clinical settings. After culturing, plasmids from different samples were isolated and paired-end sequenced using Miseq.

I proposed the following sample-wise pipeline for identification of anti-microbial genes, plasmids and resisted drugs :

2 separate fastq files per sample ===> de-novo assembly using plasmidSpades on PATRIC online service ===> upload contig files to the following web-based tools:

1. kmerFinder & PlasmidFinder for plasmids identification.
2. kmerResistance for antimicrobial genes identification.

Can someone validate this workflow? will it eventually help me identify anti-microbial genes and plasmids present in each sample? How can I improve/optimise it ?

I've just joined the lab and this is the first project I get involved in. Any suggestions or notes will be highly appreciated.

Thanks in advance.