Importing Datasets

Hello Dear All
While I am new to Qiime 2, infact a beginner.
I have fasta file data sets with three samples, the data is already demultiplexed.
Please let me know how to import this data and how to combine these sequenes ( while in qiime 1 we were having a command add_qiime_labels).
how to do it here

Hi @divyaprince321,

There is no equivalent action in QIIME 2. Based on your description of the data, it sounds like some pre-processing (including demultiplexing) has already been done and the data are now in a format that would be difficult to use in QIIME 2 (e.g., all denoising methods in QIIME 2 use fastq data). My recommendation is to either:

  1. use OTU clustering or denoising methods outside of QIIME 2, and import as a feature table. E.g., it sounds like you are using a qiime1 workflow currently — you could continue to use qiime1 for clustering etc, then import the OTU table to QIIME 2. See the importing tutorials at for details on importing a biom-format OTU table into QIIME 2.
  2. import the fastq data into QIIME 2 and perform the analysis from the beginning in QIIME 2. See the importing tutorials at to figure out the importing strategy that is most appropriate for your data.

Good luck!

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Thank for your Concerns
Does it mean that in QIIME 2 only fastq files are processed for downstream analysis

Not at all. But the denoising methods used in QIIME 2 do require fastq. You can import other data types, e.g., a biom table, but fasta formats are only used for sequences post-denoising.

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