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The steps I have done so far:

  1. used guppy to do base calling from fast5 to fastq. In each barcode file I have 1960 fastq files which I have merged.
  2. 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

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