Can ARIBA AMR tool be tweaked to support long reads inputs (eg-Oxford Nanopore)?

Question

[varunsreeraj]

Hi,

As my master thesis project, I was wondering if I could tweak the AMR finding tool ARIBA pipeline to accept long read as input. I could not find any useful resources related to that.

My first hunch as a bioinformatics student is to achieve this is by

• incorporating minimap2 to map the reads to the cluster.
• changing the assembler from fermilite to a long read assembler such as Flye or miniasm.

I would be grateful for any insights or ideas regarding my query. Or is this an unachievable feat.

Thanks in advance.

[AHerik]

Hi, did you ever figure this out? I'm working on a similar project.