Demultiplex - No barcodes and Forward Reads

Dear All,

I am having some issues during the demultiplex stage:

qiime demux emp-single
–i-seqs emp-single-end-sequences.qza
–m-barcodes-file sample-metadata.tsv
–m-barcodes-column BarcodeSequence
–o-per-sample-sequences demux.qza
–o-error-correction-details demux-details.qza

Q1- Is there any method to demultiplex without associate to barcode (In Qiime 1.9.0 I used the –i folderpairedsequence –o outputfolder –demultiplexing-method sampleid-by-file? Is there any similar command like this one in QIIME 2?
I have a folder with the paired files and another with the Mapping File (Metadata).
How can I do the demultiplex without the metadata and barcode files, like this command in QIIME 1.9.2

I would greatly appreciate for any clarification.


Hello Andre,

Good afternoon.

Yes! Check out the import guide for the fastq manifest format, as it works a lot like the script and gives you even more control over sample names.

Let us know if you have any questions!


Dear Colin,

In this case what would be the similar command in QIIME 2 for the case below? –i folderpairedsequence –o outputfolder –demultiplexing-method sampleid-by-file

Yes! The command would be something like

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path pe-33-manifest.tsv \
  --output-path paired-end-demux.qza \
  --input-format PairedEndFastqManifestPhred33V2

Note that instead of passing a folder, like folderpairedsequence, you list the files in that folder inside of the pe-33-manifest.tsv file.

(All the details are in the folder I linked to above :wink: )


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