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AMR tools for low-yield long read sequencing (MinION)

Hello,

I have samples from patients, with low yields (~200 kb) from Minion, and I'm playing around with several different AMR tools. When I run my data through ResFinder, I get 0 resistance genes. These samples are from ICU patients, and therefore some level of resistance should be expected. My question is, how should I be trouble shooting? Are more reads required?

Additionally, some other AMR detection/prediction tools (e.g., ABRicate) require fasta as input (only contigs). Can I simply convert the fastq files I have using a tool like "poretools fasta", "fq2fa from IDBA assembler"

Thank you!

metagenomics amr resfinder minion
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updated by colindaven colindaven • written by AHerik • AHerik

How many reads do you have ? It sounds way too low. Can you assemble these genomes with Flye etc ? It sounds like you need to sequence a lot, lot more.

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written by colindaven colindaven

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