Appendix: Examples illustrating importing data into QIIME 2
Contents
12. Appendix: Examples illustrating importing data into QIIME 2¶
This document will ultimately pull content from the QIIME 2 documentation’s importing guide. Refer there for now.
12.1. Discovering the available importable semantic types¶
Plugins define semantic types, so the semantic types that can be imported depends on what plugins you have installed. To discover what semantic types can be imported in your QIIME 2 deployment, you can run the following command:
qiime tools import --show-importable-types
Bowtie2Index
DeblurStats
DistanceMatrix
EMPPairedEndSequences
EMPSingleEndSequences
ErrorCorrectionDetails
FeatureData[AlignedSequence]
FeatureData[Differential]
FeatureData[Importance]
FeatureData[PairedEndSequence]
FeatureData[Sequence]
FeatureData[Taxonomy]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[Design]
FeatureTable[Frequency]
FeatureTable[PercentileNormalized]
FeatureTable[PresenceAbsence]
FeatureTable[RelativeFrequency]
Hierarchy
MultiplexedPairedEndBarcodeInSequence
MultiplexedSingleEndBarcodeInSequence
PCoAResults
Phylogeny[Rooted]
Phylogeny[Unrooted]
Placements
QualityFilterStats
RawSequences
SampleData[AlphaDiversity]
SampleData[BooleanSeries]
SampleData[ClassifierPredictions]
SampleData[DADA2Stats]
SampleData[FirstDifferences]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[Probabilities]
SampleData[RegressorPredictions]
SampleData[SequencesWithQuality]
SampleData[Sequences]
SampleEstimator[Classifier]
SampleEstimator[Regressor]
SeppReferenceDatabase
TaxonomicClassifier
UchimeStats
12.2. Discovering the available importable formats¶
Plugins define file types (or formats) as well. To discover what formats can be imported from in your QIIME 2 deployment, you can run the following command:
qiime tools import --show-importable-formats
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
AlphaDiversityDirectoryFormat
AlphaDiversityFormat
BIOMV100DirFmt
BIOMV100Format
BIOMV210DirFmt
BIOMV210Format
BooleanSeriesDirectoryFormat
BooleanSeriesFormat
Bowtie2IndexDirFmt
CasavaOneEightLanelessPerSampleDirFmt
CasavaOneEightSingleLanePerSampleDirFmt
DADA2StatsDirFmt
DADA2StatsFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
DeblurStatsDirFmt
DeblurStatsFmt
DifferentialDirectoryFormat
DifferentialFormat
DistanceMatrixDirectoryFormat
EMPPairedEndCasavaDirFmt
EMPPairedEndDirFmt
EMPSingleEndCasavaDirFmt
EMPSingleEndDirFmt
ErrorCorrectionDetailsDirFmt
FastqGzFormat
FirstDifferencesDirectoryFormat
FirstDifferencesFormat
HeaderlessTSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
ImportanceDirectoryFormat
ImportanceFormat
LSMatFormat
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedSingleEndBarcodeInSequenceDirFmt
NewickDirectoryFormat
NewickFormat
OrdinationDirectoryFormat
OrdinationFormat
PairedDNASequencesDirectoryFormat
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64
PairedEndFastqManifestPhred64V2
PlacementsDirFmt
PlacementsFormat
PredictionsDirectoryFormat
PredictionsFormat
ProbabilitiesDirectoryFormat
ProbabilitiesFormat
QIIME1DemuxDirFmt
QIIME1DemuxFormat
QualityFilterStatsDirFmt
QualityFilterStatsFmt
SampleEstimatorDirFmt
SeppReferenceDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64
SingleEndFastqManifestPhred64V2
SingleLanePerSamplePairedEndFastqDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
TSVTaxonomyDirectoryFormat
TSVTaxonomyFormat
TaxonomicClassiferTemporaryPickleDirFmt
UchimeStatsDirFmt
UchimeStatsFmt