The steps i have done so far

  • used guppy to do base calling from fast5 to fastq so what i see is in each barcode file i have 1960 fastq files which i have merged.
  • The i did trim the fastq files using NanoFilt
  • Now what i saw from various resources is they are going for 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 which were filtered in tools like kraken for taxonomic classification..

Any help or suggestion would be really appreciated

  • $\begingroup$ You can proceed directly with the taxonomy classification, QIIME2 or Kraken2 if you prefer. $\endgroup$
    – zorbax
    Jun 22 '20 at 12:29
  • $\begingroup$ okay so denovo assembly not necessary as such? $\endgroup$
    – kcm
    Jun 23 '20 at 10:45

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