Generate ASV table for nanopore data

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1

Hello,

I have 16s data sequenced using using nanopore platform.
I have some trouble to process the data using and deblur for denoising and filtering.
So I use Porechop and fastp in the Galaxy, then import the data back in Qiime.

Is there any way I can produce ASV table like this:

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Thanks

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2

Hey @zahir,

Looks like you made it through read processing!

To convert, you will want to run this command (inside a qiime2 environment):

biom convert -i <YOUR ASV TABLE.TSV/TXT> -o converted.biom --to-hdf5

Then, to double check things run:

biom summarize-table -i converted.biom

You should see all of your samples and things should look familiar.

Assuming that went well, you can import via this command:

qiime tools import \
  --input-path converted.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path feature-table.qza

That should get you on your way!

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3

Thanks a lot for your response
But I think I dont make my question clear.

Actually, I already import my processed read into qiime using 'qiime tools import'

qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path manifest_16s_dr.tsv \
  --output-path single-end-demux.qza \
  --input-format SingleEndFastqManifestPhred33V2

qiime demux summarize \
  --i-data single-end-demux.qza \
  --o-visualization demux.qzv

After that I use vsearch to dereplicate and cluster my reads

qiime vsearch dereplicate-sequences \
  --i-sequences single-end-demux.qza \
  --o-dereplicated-table table.qza \
  --o-dereplicated-sequences rep-seqs.qza

qiime vsearch cluster-features-closed-reference \
  --i-table table.qza \
  --i-sequences rep-seqs.qza \
  --i-reference-sequences 85_otus.qza \
  --p-perc-identity 0.85 \
  --o-clustered-table table-cr-85.qza \
  --o-clustered-sequences rep-seqs-cr-85.qza \
  --o-unmatched-sequences unmatched-cr-85.qza

qiime feature-table summarize \
  --i-table table-cr-85.qza \
  --o-visualization table-cr-85.qzv \
  --m-sample-metadata-file metadata-avg.tsv
qiime feature-table tabulate-seqs \
  --i-data rep-seqs-cr-85.qza \
  --o-visualization rep-seqs-cr-85.qzv

here is the .qzv files generated

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image
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So from here how can i generate OTU/ASV table like this:

image
image1582×932 50.3 KB

Thanks

4

Oh I see. You already have! That's what the feature-table is.

So if you wanted a TSV, you would basically run my steps in reverse:

Export the table (you can technically just unzip it and look in <weird UUID directory>/data/):

qiime tools export \
  --input-path table-cr-85.qza \
  --output-path table-cr-85.biom \
  --output-format BIOMV210Format

Then use biom to convert to tsv:

biom convert -i able-cr-85.biom -o table-cr-85.tsv --to-tsv
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5

Thanks a lot for ur help
much appreciate it

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