Hello reader.
Asking this question again because i couldn’t find a proper answer or suggestion.
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 than 3% reads are actually >Q20.
I previously used Flye genome assembler version: 2.9.5 with 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
Thank you.
First, I recommend to do basecalling in sup mode instead of hac. You'll likely have a better assembly with sup reads.
Regarding your question: I suggest to try both options and see which one will result in a better assembly. I suppose that the assemblies will be of similar quality, but the assembly with --nano-hq will take less time.
Also, in addition to Flye it's probably worth trying the latest release of Hifiasm with option "--ont".
Hello, Thanks for the response.
which dorado version to use as there are two different latest builds. v0.7.4 and v0.8.3
also, will Hifiasm work for haploid fungal genomes ? as far as i know it is built for diploid genomes.
I have tested canu and nextDenovo but flye yeilded better results.
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