This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2024.10.0
website: https://github.com/qiime2/q2-types
user support:
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions

NameTypeShort Description
partition-sample-data-magsmethodPartition MAGs
partition-orthologsmethodPartition orthologs
collate-sample-data-magsmethodCollate MAGs
partition-feature-data-magsmethodPartition MAGs
collate-feature-data-magsmethodCollate MAGs
collate-orthologsmethodCollate orthologs
collate-ortholog-annotationsmethodCollate ortholog annotations.

Artifact Classes

Bowtie2Index
DistanceMatrix
FeatureData[Taxonomy]
FeatureData[Sequence]
FeatureData[RNASequence]
FeatureData[PairedEndSequence]
FeatureData[PairedEndRNASequence]
FeatureData[AlignedSequence]
FeatureData[AlignedRNASequence]
FeatureData[Differential]
FeatureData[ProteinSequence]
FeatureData[AlignedProteinSequence]
FeatureData[BLAST6]
FeatureData[SequenceCharacteristics]
FeatureData[MAG]
FeatureData[Contig]
FeatureData[SingleBowtie2Index]
FeatureMap[MAGtoContigs]
FeatureTable[Frequency]
FeatureTable[RelativeFrequency]
FeatureTable[PresenceAbsence]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[PercentileNormalized]
FeatureTable[Design]
FeatureTable[Normalized]
GenomeData[Genes]
GenomeData[Proteins]
GenomeData[Loci]
GenomeData[Orthologs]
GenomeData[DNASequence]
GenomeData[NOG]
SampleData[Orthologs]
SampleData[NOG]
KaijuDB
SampleData[Kraken2Report]
FeatureData[Kraken2Report]
SampleData[Kraken2Output]
FeatureData[Kraken2Output]
Kraken2DB
Kraken2DBReport
BrackenDB
ImmutableMetadata
MultiplexedSingleEndBarcodeInSequence
MultiplexedPairedEndBarcodeInSequence
RawSequences
EMPSingleEndSequences
EMPPairedEndSequences
ErrorCorrectionDetails
PCoAResults
ProcrustesStatistics
SampleData[Sequences]
SampleData[SequencesWithQuality]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[MAGs]
SampleData[Contigs]
SampleData[SingleBowtie2Index]
SampleData[MultiBowtie2Index]
SampleData[AlignmentMap]
FeatureData[AlignmentMap]
SampleData[MultiAlignmentMap]
ProfileHMM[PressedProtein]
ProfileHMM[PressedDNA]
ProfileHMM[PressedRNA]
ProfileHMM[SingleProtein]
ProfileHMM[SingleDNA]
ProfileHMM[SingleRNA]
ProfileHMM[MultipleProtein]
ProfileHMM[MultipleDNA]
ProfileHMM[MultipleRNA]
ReferenceDB[Eggnog]
ReferenceDB[Diamond]
ReferenceDB[NCBITaxonomy]
ReferenceDB[EggnogProteinSequences]
SampleData[AlphaDiversity]
Phylogeny[Unrooted]
Phylogeny[Rooted]
Hierarchy

Formats

Bowtie2IndexDirFmt
LSMatFormat
DistanceMatrixDirectoryFormat
TSVTaxonomyFormat
TSVTaxonomyDirectoryFormat
HeaderlessTSVTaxonomyFormat
HeaderlessTSVTaxonomyDirectoryFormat
TaxonomyFormat
TaxonomyDirectoryFormat
FASTAFormat
DNAFASTAFormat
DNASequencesDirectoryFormat
PairedDNASequencesDirectoryFormat
AlignedDNAFASTAFormat
AlignedDNASequencesDirectoryFormat
DifferentialFormat
DifferentialDirectoryFormat
ProteinFASTAFormat
AlignedProteinFASTAFormat
MixedCaseProteinFASTAFormat
MixedCaseAlignedProteinFASTAFormat
ProteinSequencesDirectoryFormat
AlignedProteinSequencesDirectoryFormat
MixedCaseProteinSequencesDirectoryFormat
MixedCaseAlignedProteinSequencesDirectoryFormat
RNAFASTAFormat
RNASequencesDirectoryFormat
AlignedRNAFASTAFormat
AlignedRNASequencesDirectoryFormat
PairedRNASequencesDirectoryFormat
BLAST6Format
BLAST6DirectoryFormat
MixedCaseDNAFASTAFormat
MixedCaseDNASequencesDirectoryFormat
MixedCaseRNAFASTAFormat
MixedCaseRNASequencesDirectoryFormat
MixedCaseAlignedDNAFASTAFormat
MixedCaseAlignedDNASequencesDirectoryFormat
MixedCaseAlignedRNAFASTAFormat
MixedCaseAlignedRNASequencesDirectoryFormat
SequenceCharacteristicsFormat
SequenceCharacteristicsDirectoryFormat
MAGSequencesDirFmt
MAGtoContigsFormat
MAGtoContigsDirFmt
BIOMV100Format
BIOMV210Format
BIOMV100DirFmt
BIOMV210DirFmt
GenesDirectoryFormat
ProteinsDirectoryFormat
LociDirectoryFormat
GenomeSequencesDirectoryFormat
OrthologFileFmt
SeedOrthologDirFmt
OrthologAnnotationDirFmt
GFF3Format
KaijuDBDirectoryFormat
KaijuIndexFormat
Kraken2ReportFormat
Kraken2OutputFormat
Kraken2DBFormat
Kraken2DBReportFormat
Kraken2ReportDirectoryFormat
Kraken2OutputDirectoryFormat
Kraken2DBDirectoryFormat
Kraken2DBReportDirectoryFormat
BrackenDBFormat
BrackenDBDirectoryFormat
ImmutableMetadataFormat
ImmutableMetadataDirectoryFormat
MultiplexedSingleEndBarcodeInSequenceDirFmt
MultiplexedPairedEndBarcodeInSequenceDirFmt
MultiplexedFastaQualDirFmt
EMPMultiplexedDirFmt
ErrorCorrectionDetailsDirFmt
ErrorCorrectionDetailsFmt
EMPSingleEndDirFmt
EMPSingleEndCasavaDirFmt
EMPPairedEndDirFmt
EMPPairedEndCasavaDirFmt
OrdinationFormat
OrdinationDirectoryFormat
ProcrustesStatisticsFmt
ProcrustesStatisticsDirFmt
FastqManifestFormat
FastqAbsolutePathManifestFormat
YamlFormat
FastqGzFormat
CasavaOneEightSingleLanePerSampleDirFmt
CasavaOneEightLanelessPerSampleDirFmt
SingleLanePerSampleSingleEndFastqDirFmt
SingleLanePerSamplePairedEndFastqDirFmt
SingleEndFastqManifestPhred33
SingleEndFastqManifestPhred64
PairedEndFastqManifestPhred33
PairedEndFastqManifestPhred64
SingleEndFastqManifestPhred33V2
SingleEndFastqManifestPhred64V2
PairedEndFastqManifestPhred33V2
PairedEndFastqManifestPhred64V2
QIIME1DemuxFormat
QIIME1DemuxDirFmt
SampleIdIndexedSingleEndPerSampleDirFmt
MultiFASTADirectoryFormat
MultiMAGSequencesDirFmt
ContigSequencesDirFmt
MultiBowtie2IndexDirFmt
BAMFormat
BAMDirFmt
MultiBAMDirFmt
MultiMAGManifestFormat
ProteinMultipleProfileHmmFileFmt
ProteinSingleProfileHmmFileFmt
RNAMultipleProfileHmmFileFmt
RNASingleProfileHmmFileFmt
DNAMultipleProfileHmmFileFmt
DNASingleProfileHmmFileFmt
PressedProfileHmmsDirectoryFmt
ProteinSingleProfileHmmDirectoryFmt
ProteinMultipleProfileHmmDirectoryFmt
DNASingleProfileHmmDirectoryFmt
DNAMultipleProfileHmmDirectoryFmt
RNASingleProfileHmmDirectoryFmt
RNAMultipleProfileHmmDirectoryFmt
EggnogRefTextFileFmt
EggnogRefBinFileFmt
EggnogRefDirFmt
DiamondDatabaseFileFmt
DiamondDatabaseDirFmt
NCBITaxonomyNodesFormat
NCBITaxonomyNamesFormat
NCBITaxonomyBinaryFileFmt
NCBITaxonomyDirFmt
EggnogProteinSequencesDirFmt
AlphaDiversityFormat
AlphaDiversityDirectoryFormat
NewickFormat
NewickDirectoryFormat