The steps I have done so far:
- used guppy to do base calling from fast5 to fastq. In each barcode file I have 1960 fastq files which I have merged.
- trimmed the fastq files using NanoFilt
Now what I see from various resources is they do de-novo assembly using tools like canu followed by minimap.
So is it needed to do de-novo assembly?
Or I can simply use my fastq files and process them using tools like kraken for taxonomic classification?
Any help or suggestion would be really appreciated