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qiime2 tools export (version 2023.5.0+dist.h193f7cc9.2)

QIIME 2: tools export

Export a QIIME 2 artifact to different formats


  1. Select the QZA you would like to export. Once selected, two fields will update indicating the type and format of this QZA.
  2. If you wish to change the output format, first provide the same type as the QZA (which is shown above). This will filter the avaiable formats.
  3. Select the format you desire. Some limited documentation is available on these formats below.

IMPORTANT: if you select the wrong type when exporting, you will recieve an error suggesting "No transformation from <X> to <Y>".


These formats have documentation available.


QIIME 1 demultiplexed FASTA format.

The QIIME 1 demultiplexed FASTA format is the default output format of and The file output by QIIME 1 is named seqs.fna; this filename is sometimes associated with the file format itself due to its widespread usage in QIIME 1.

The format is documented here:

Format details:

  • FASTA file with exactly two lines per record: header and sequence. Each sequence must span exactly one line and cannot be split across multiple lines.
  • The ID in each header must follow the format <sample-id>_<seq-id>. <sample-id> is the identifier of the sample the sequence belongs to, and <seq-id> is an identifier for the sequence within its sample. In QIIME 1, <seq-id> is typically an incrementing integer starting from zero, but any non-empty value can be used here, as long as the header IDs remain unique throughout the file. Note: <sample-id> may contain sample IDs that contain underscores; the rightmost underscore will used to delimit sample and sequence IDs.
  • Descriptions in headers are permitted and ignored.
  • Header IDs must be unique within the file.
  • Each sequence must be DNA and cannot be empty.


Format for a 2+ column TSV file with an expected minimal header.

The only header recognized by this format is:

Feature ID<tab>Taxon

Optionally followed by other arbitrary columns.

This format supports blank lines. The expected header must be the first non-blank line. In addition to the header, there must be at least one line of data.


A gzipped fastq file.

Additional formats without documentation:

  • FirstDifferencesFormat
  • DecontamScoreDirFmt
  • OrdinationDirectoryFormat
  • EMPPairedEndDirFmt
  • ImmutableMetadataFormat
  • PredictionsDirectoryFormat
  • AlphaDiversityDirectoryFormat
  • DataLoafPackageDirFmt
  • AlignedDNAFASTAFormat
  • DADA2StatsDirFmt
  • TrueTargetsDirectoryFormat
  • UchimeStatsFmt
  • BLAST6Format
  • PairedDNASequencesDirectoryFormat
  • QIIME1DemuxDirFmt
  • QualityFilterStatsFmt
  • DADA2StatsFormat
  • AlignedProteinFASTAFormat
  • PlacementsFormat
  • NewickFormat
  • ProbabilitiesDirectoryFormat
  • ErrorCorrectionDetailsDirFmt
  • ProteinFASTAFormat
  • RNAFASTAFormat
  • MultiplexedSingleEndBarcodeInSequenceDirFmt
  • BooleanSeriesFormat
  • LSMatFormat
  • ImportanceDirectoryFormat
  • DeblurStatsFmt
  • AlignedRNASequencesDirectoryFormat
  • QualityFilterStatsDirFmt
  • TaxonomicClassiferTemporaryPickleDirFmt
  • BooleanSeriesDirectoryFormat
  • DifferentialDirectoryFormat
  • DNAFASTAFormat
  • ProcrustesStatisticsFmt
  • PlacementsDirFmt
  • EMPSingleEndDirFmt
  • DecontamScoreFormat
  • BIOMV210DirFmt
  • ImmutableMetadataDirectoryFormat
  • AlignedDNASequencesDirectoryFormat
  • TSVTaxonomyDirectoryFormat
  • OrdinationFormat
  • FirstDifferencesDirectoryFormat
  • Bowtie2IndexDirFmt
  • BIOMV210Format
  • SingleLanePerSampleSingleEndFastqDirFmt
  • SampleEstimatorDirFmt
  • PairedRNASequencesDirectoryFormat
  • CasavaOneEightSingleLanePerSampleDirFmt
  • AlignedProteinSequencesDirectoryFormat
  • UchimeStatsDirFmt
  • NewickDirectoryFormat
  • SingleLanePerSamplePairedEndFastqDirFmt
  • DifferentialFormat
  • ProteinSequencesDirectoryFormat
  • RNASequencesDirectoryFormat
  • MultiplexedPairedEndBarcodeInSequenceDirFmt
  • AlphaDiversityFormat
  • DistanceMatrixDirectoryFormat
  • ArtificialGroupingFormat
  • ArtificialGroupingDirectoryFormat
  • ProbabilitiesFormat
  • DeblurStatsDirFmt
  • SeppReferenceDirFmt
  • ImportanceFormat
  • BLAST6DirectoryFormat
  • AlignedRNAFASTAFormat
  • DNASequencesDirectoryFormat
  • ProcrustesStatisticsDirFmt
  • PredictionsFormat