How can I generate ASV file format from nanopore sequencing data for Picrust2 input file?

[Rasmita Mishra]

Hi,

I am looking for a way to get functional analysis with 16s long reads. For the abundance classification, I am using the Kraken2 tool. And then for the biome file, I am using the Kraken biome and generating a biome format table with the first column as taxaID and other columns for sample abundance.

but I am unable to generate an ASV file format table and an ASV_ID associated sequence fasta file which are needed to picruste2 as the input file.

Is there a way I could go ahead with doing functional annotations with current data?

Or is there any other way to generate ASV file from nanopore sequencing data?

Any help is appreciated!

Thanks in advance!

[Gavin Douglas]

Hey there,

You won’t be able to use the kraken2 output to make predictions (with PICRUSt2 anyway), as it does require actual 16S DNA sequences. I’m not aware of any nanopore-specific approach for generating ASVs, but I would look into DADA2 and see if there is an option using that tool. I would be surprised if this hadn’t been discussed on the QIIME 2 forum as well.

Sorry I can’t be of more help!

Gavin

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[Ana Benavides]

Hi :),

I would like to know if you found a solution? I'm trying to analyze a lot of metabarcoding data. I used Kraken 2 for taxonomic assignment and have the .biom file, but I don't know how to generate the other input, the .fasta file.