Hi reader,

I have some nanopore sequenced fungal sample. Sequenced with R10.4 cell and LSK114 kit.

Some initial Information

• Median Length average: 8055bp
• N50 on average: 11109
• Meadian Quality average: 16.7

Question 1: I am not sure about the term Error-Rate in sequencing. Can you guide or point me to direction where I can read about it and calculate it in my data sets ?

The Sequencing company already basecalled the data with Dorado and provided fastQ files as pass/fail. I want to generate assemblies so using fastQ-Pass files for downstream analysis.

I have used Porechop to remove adapters and Chopper to remove reads with Q<10 and Length<2000.

I am using Flye v-2.9.5-b1801 for genome assemblies. I have question regarding selecting the read-type option.

Question 2: out of these two which one is more suitable for my data .

--nano-raw path [path ...]
                        ONT regular reads, pre-Guppy5 (<20% error)
--nano-hq path [path ...]
                        ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error)

Also, Is the --scaffold option in Flye assembler recomended to use ?

Thank you.