Nano-Raw vs Nano-HQ options

[ufaroooq]

Hello, Thankyou for such a great tools.

I have some nanopore sequenced fungal sample. Sequenced with R10.4 cell and LSK114 kit.
Basecalling was performed using dorado and from fastQ files i found basecall_model_version_id=dna_r10.4.1_e8.2_400bps_hac@v4.2.0

• Median Q-score across all samples is between 16-17
• Median Read-length across all samples is between 7000-9000
• in all samples less tha 3% reads are actually >Q20.

I previously usied nano-raw option for assembly generation but now i see some papers which have data sequenced with same nanopore cell and chemistry and they used nano-hq option.

This makes me confused on which option should be used for my data.

Can you share some insights on this. Will be a great assistance.

Previous command I used
flye --nano-raw NP01_chopper.fastq --out-dir ./flye_assemblies/NP01/ --threads 45 --genome-size 60m --iterations 2 --scaffold

[mikolmogorov]

Hi - nano-hq should work fine for your data!