Entering edit mode
8 weeks ago
AHerik
▴
20
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!
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.