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Artifact Classes

quality-control


FeatureData[DecontamScore]

plugin: quality-control
format: DecontamScoreDirFmt
transformers:
viewimportexport
DecontamScoreDirFmt
DecontamScoreFormat

fragment-insertion


Placements

plugin: fragment-insertion
format: PlacementsDirFmt
transformers:
viewimportexport
PlacementsDirFmt
PlacementsFormat

SeppReferenceDatabase

plugin: fragment-insertion
format: SeppReferenceDirFmt
transformers:
viewimportexport
SeppReferenceDirFmt

metadata


SampleData[ArtificialGrouping]


fondue


SRAMetadata

SRAFailedIDs

plugin: fondue
format: SRAFailedIDsDirFmt
transformers:
viewimportexport
SRAFailedIDsFormat
SRAFailedIDsDirFmt

NCBIAccessionIDs


sample-classifier


SampleEstimator[Classifier]

plugin: sample-classifier
format: SampleEstimatorDirFmt
transformers:
viewimportexport
SampleEstimatorDirFmt

SampleEstimator[Regressor]

plugin: sample-classifier
format: SampleEstimatorDirFmt
transformers:
viewimportexport
SampleEstimatorDirFmt

SampleData[BooleanSeries]

SampleData[RegressorPredictions]

plugin: sample-classifier
format: PredictionsDirectoryFormat
transformers:

SampleData[ClassifierPredictions]

plugin: sample-classifier
format: PredictionsDirectoryFormat
transformers:

FeatureData[Importance]

plugin: sample-classifier
format: ImportanceDirectoryFormat
transformers:
viewimportexport
ImportanceDirectoryFormat
ImportanceFormat

SampleData[Probabilities]

SampleData[TrueTargets]

plugin: sample-classifier
format: TrueTargetsDirectoryFormat
transformers:

rescript


FeatureData[SILVATaxonomy]

plugin: rescript
format: SILVATaxonomyDirectoryFormat
transformers:

FeatureData[SILVATaxidMap]

plugin: rescript
format: SILVATaxidMapDirectoryFormat
transformers:

composition


FeatureData[DifferentialAbundance]

plugin: composition
format: DataLoafPackageDirFmt
transformers:
viewimportexport
DataLoafPackageDirFmt

FeatureData[ANCOMBC2Output]

plugin: composition
format: ANCOMBC2OutputDirFmt
transformers:
viewimportexport
ANCOMBC2OutputDirFmt

deblur


DeblurStats

plugin: deblur
format: DeblurStatsDirFmt
transformers:
viewimportexport
DeblurStatsDirFmt
DeblurStatsFmt

dada2


SampleData[DADA2Stats]

plugin: dada2
format: DADA2StatsDirFmt
transformers:
viewimportexport
DADA2StatsFormat
DADA2StatsDirFmt

DADA2BaseTransitionStats


vsearch


UchimeStats

plugin: vsearch
format: UchimeStatsDirFmt
transformers:
viewimportexport
UchimeStatsDirFmt
UchimeStatsFmt

quality-filter


QualityFilterStats

plugin: quality-filter
format: QualityFilterStatsDirFmt
transformers:

feature-classifier


BLASTDB

plugin: feature-classifier
format: BLASTDBDirFmtV5
transformers:
viewimportexport
BLASTDBDirFmtV5

TaxonomicClassifier


longitudinal


SampleData[FirstDifferences]


types


Bowtie2Index

An index of sequences for Bowtie 2 to search against.

plugin: types
format: Bowtie2IndexDirFmt
transformers:
viewimportexport
Bowtie2IndexDirFmt

DistanceMatrix

A symmetric matrix representing distances between entities.

plugin: types
format: DistanceMatrixDirectoryFormat
transformers:
viewimportexport
LSMatFormat
DistanceMatrixDirectoryFormat

FeatureData[Taxonomy]

Hierarchical metadata or annotations associated with a set of features. This can contain one or more hierarchical levels, and annotations can be anything (e.g., taxonomy of organisms, functional categorization of gene families, ...) as long as it is strictly hierarchical.

plugin: types
format: TSVTaxonomyDirectoryFormat
transformers:

FeatureData[Sequence]

Unaligned DNA sequences associated with a set of feature identifiers (e.g., ASV sequences or OTU representative sequence). Exactly one sequence is associated with each feature identifier.

plugin: types
format: DNASequencesDirectoryFormat
transformers:

FeatureData[RNASequence]

Unaligned RNA sequences associated with a set of feature identifiers. Exactly one sequence is associated with each feature identifier.

plugin: types
format: RNASequencesDirectoryFormat
transformers:

FeatureData[PairedEndSequence]

plugin: types
format: PairedDNASequencesDirectoryFormat
transformers:
viewimportexport
PairedDNASequencesDirectoryFormat

FeatureData[PairedEndRNASequence]

plugin: types
format: PairedRNASequencesDirectoryFormat
transformers:
viewimportexport
PairedRNASequencesDirectoryFormat

FeatureData[AlignedSequence]

Aligned DNA sequences associated with a set of feature identifiers (e.g., aligned ASV sequences or OTU representative sequence). Exactly one sequence is associated with each feature identifier.

plugin: types
format: AlignedDNASequencesDirectoryFormat
transformers:

FeatureData[AlignedRNASequence]

Aligned RNA sequences associated with a set of feature identifiers. Exactly one sequence is associated with each feature identifier.

plugin: types
format: AlignedRNASequencesDirectoryFormat
transformers:

FeatureData[Differential]

plugin: types
format: DifferentialDirectoryFormat
transformers:

FeatureData[ProteinSequence]

Unaligned protein sequences associated with a set of feature identifiers. Exactly one sequence is associated with each feature identifier.

plugin: types
format: ProteinSequencesDirectoryFormat
transformers:

FeatureData[AlignedProteinSequence]

Aligned protein sequences associated with a set of feature identifiers. Exactly one sequence is associated with each feature identifier.

plugin: types
format: AlignedProteinSequencesDirectoryFormat
transformers:

FeatureData[BLAST6]

BLAST results associated with a set of feature identifiers.

plugin: types
format: BLAST6DirectoryFormat
transformers:
viewimportexport
BLAST6DirectoryFormat
BLAST6Format

FeatureData[SequenceCharacteristics]

Characteristics of sequences (e.g., the length of a gene in basepairs).

plugin: types
format: SequenceCharacteristicsDirectoryFormat
transformers:

FeatureData[MAG]

plugin: types
format: MAGSequencesDirFmt
transformers:
viewimportexport
MAGSequencesDirFmt

FeatureData[Contig]

plugin: types
format: ContigSequencesDirFmt
transformers:
viewimportexport
ContigSequencesDirFmt

FeatureData[SingleBowtie2Index]

plugin: types
format: Bowtie2IndexDirFmt
transformers:
viewimportexport
Bowtie2IndexDirFmt

FeatureMap[MAGtoContigs]

plugin: types
format: MAGtoContigsDirFmt
transformers:
viewimportexport
MAGtoContigsFormat
MAGtoContigsDirFmt

FeatureMap[TaxonomyToContigs]

plugin: types
format: FeatureMapDirFmt
transformers:
viewimportexport
FeatureMapFormat
FeatureMapDirFmt

FeatureMap[FunctionToContigs]

plugin: types
format: FeatureMapDirFmt
transformers:
viewimportexport
FeatureMapFormat
FeatureMapDirFmt

FeatureTable[Frequency]

A feature table (e.g., samples by ASVs) where each value in the matrix is a whole number greater than or equal to 0 representing the frequency or count of a feature in the corresponding sample. These data should be raw (not normalized) counts.

plugin: types
format: BIOMV210DirFmt
transformers:

FeatureTable[RelativeFrequency]

A feature table (e.g., samples by ASVs) where each value in the matrix is a real number greater than or equal to 0.0 and less than or equal to 1.0 representing the proportion of the sample that is composed of that feature. The feature values for each sample should sum to 1.0.

plugin: types
format: BIOMV210DirFmt
transformers:

FeatureTable[PresenceAbsence]

A feature table (e.g., samples by ASVs) where each value indicates is a boolean indication of whether the feature is observed in the sample or not.

plugin: types
format: BIOMV210DirFmt
transformers:

FeatureTable[Balance]

FeatureTable[Composition]

A feature table (e.g., samples by ASVs) where each value in the matrix is a whole number greater than 0 representing the frequency or count of a feature in the corresponding sample. These data are typically not raw counts, having been transformed in some way to exclude zero counts.

plugin: types
format: BIOMV210DirFmt
transformers:

FeatureTable[PercentileNormalized]

FeatureTable[Design]

FeatureTable[Normalized]

A feature table that was normalized.

plugin: types
format: BIOMV210DirFmt
transformers:

FeatureTable[Unconstrained]

A feature table containing real-valued feature measurements represented in Euclidean space without constant-sum (compositional) constraints.

plugin: types
format: BIOMV210DirFmt
transformers:

GenomeData[Genes]

plugin: types
format: GenesDirectoryFormat
transformers:
viewimportexport
GenesDirectoryFormat

GenomeData[Proteins]

plugin: types
format: ProteinsDirectoryFormat
transformers:
viewimportexport
ProteinsDirectoryFormat

GenomeData[Loci]

plugin: types
format: LociDirectoryFormat
transformers:
viewimportexport
LociDirectoryFormat

GenomeData[Orthologs]

plugin: types
format: SeedOrthologDirFmt
transformers:
viewimportexport
SeedOrthologDirFmt

GenomeData[DNASequence]

plugin: types
format: GenomeSequencesDirectoryFormat
transformers:
viewimportexport
GenomeSequencesDirectoryFormat

GenomeData[NOG]

plugin: types
format: OrthologAnnotationDirFmt
transformers:
viewimportexport
OrthologAnnotationDirFmt

SampleData[Orthologs]

plugin: types
format: SeedOrthologDirFmt
transformers:
viewimportexport
SeedOrthologDirFmt

SampleData[NOG]

plugin: types
format: OrthologAnnotationDirFmt
transformers:
viewimportexport
OrthologAnnotationDirFmt

KaijuDB

plugin: types
format: KaijuDBDirectoryFormat
transformers:
viewimportexport
KaijuDBDirectoryFormat

SampleData[Kraken2Report]

plugin: types
format: Kraken2ReportDirectoryFormat
transformers:
viewimportexport
Kraken2ReportDirectoryFormat

FeatureData[Kraken2Report]

plugin: types
format: Kraken2ReportDirectoryFormat
transformers:
viewimportexport
Kraken2ReportDirectoryFormat

SampleData[Kraken2Output]

plugin: types
format: Kraken2OutputDirectoryFormat
transformers:
viewimportexport
Kraken2OutputDirectoryFormat

FeatureData[Kraken2Output]

plugin: types
format: Kraken2OutputDirectoryFormat
transformers:
viewimportexport
Kraken2OutputDirectoryFormat

Kraken2DB

plugin: types
format: Kraken2DBDirectoryFormat
transformers:
viewimportexport
Kraken2DBDirectoryFormat

Kraken2DBReport

plugin: types
format: Kraken2DBReportDirectoryFormat
transformers:

BrackenDB

plugin: types
format: BrackenDBDirectoryFormat
transformers:
viewimportexport
BrackenDBDirectoryFormat

ImmutableMetadata

Immutable sample or feature metadata.

plugin: types
format: ImmutableMetadataDirectoryFormat
transformers:

MultiplexedSingleEndBarcodeInSequence

Multiplexed sequences (i.e., representing multiple difference samples), which are single-end reads, and which contain the barcode (i.e., index) indicating the source sample as part of the sequence read.

plugin: types
format: MultiplexedSingleEndBarcodeInSequenceDirFmt
transformers:

MultiplexedPairedEndBarcodeInSequence

Multiplexed sequences (i.e., representing multiple difference samples), which are paired-end reads, and which contain the barcode (i.e., index) indicating the source sample as part of the sequence read.

plugin: types
format: MultiplexedPairedEndBarcodeInSequenceDirFmt
transformers:

RawSequences

plugin: types
format: EMPSingleEndDirFmt
transformers:

EMPSingleEndSequences

plugin: types
format: EMPSingleEndDirFmt
transformers:

EMPPairedEndSequences

plugin: types
format: EMPPairedEndDirFmt
transformers:

ErrorCorrectionDetails

plugin: types
format: ErrorCorrectionDetailsDirFmt
transformers:

PCoAResults

The results of running principal coordinate analysis (PCoA).

plugin: types
format: OrdinationDirectoryFormat
transformers:
viewimportexport
OrdinationDirectoryFormat
OrdinationFormat

ProcrustesStatistics

The results of running Procrustes analysis.

plugin: types
format: ProcrustesStatisticsDirFmt
transformers:

SampleData[Sequences]

Collections of sequences associated with specified samples (i.e., demultiplexed sequences).

plugin: types
format: QIIME1DemuxDirFmt
transformers:

SampleData[SequencesWithQuality]

SampleData[JoinedSequencesWithQuality]

SampleData[PairedEndSequencesWithQuality]

SampleData[MAGs]

plugin: types
format: MultiMAGSequencesDirFmt
transformers:

SampleData[Contigs]

plugin: types
format: ContigSequencesDirFmt
transformers:
viewimportexport
ContigSequencesDirFmt

SampleData[SingleBowtie2Index]

plugin: types
format: Bowtie2IndexDirFmt
transformers:
viewimportexport
Bowtie2IndexDirFmt

SampleData[MultiBowtie2Index]

plugin: types
format: MultiBowtie2IndexDirFmt
transformers:
viewimportexport
MultiBowtie2IndexDirFmt

SampleData[AlignmentMap]

plugin: types
format: BAMDirFmt
transformers:
viewimportexport
BAMDirFmt

FeatureData[AlignmentMap]

plugin: types
format: BAMDirFmt
transformers:
viewimportexport
BAMDirFmt

SampleData[MultiAlignmentMap]

plugin: types
format: MultiBAMDirFmt
transformers:
viewimportexport
MultiBAMDirFmt

ProfileHMM[PressedProtein]

A collection of profile Hidden Markov Models for amino acid sequences in binary format and indexed.

plugin: types
format: PressedProfileHmmsDirectoryFmt
transformers:
viewimportexport
PressedProfileHmmsDirectoryFmt

ProfileHMM[PressedDNA]

A collection of profile Hidden Markov Models for DNA sequences in binary format and indexed.

plugin: types
format: PressedProfileHmmsDirectoryFmt
transformers:
viewimportexport
PressedProfileHmmsDirectoryFmt

ProfileHMM[PressedRNA]

A collection of profile Hidden Markov Models for RNA sequences in binary format and indexed.

plugin: types
format: PressedProfileHmmsDirectoryFmt
transformers:
viewimportexport
PressedProfileHmmsDirectoryFmt

ProfileHMM[SingleProtein]

One single profile Hidden Markov Model representing a group of related proteins.

plugin: types
format: ProteinSingleProfileHmmDirectoryFmt
transformers:

ProfileHMM[SingleDNA]

One single profile Hidden Markov Model representing a group of related DNA sequences.

plugin: types
format: DNASingleProfileHmmDirectoryFmt
transformers:
viewimportexport
DNASingleProfileHmmDirectoryFmt

ProfileHMM[SingleRNA]

One single profile Hidden Markov Model representing a group of related RNA sequences.

plugin: types
format: RNASingleProfileHmmDirectoryFmt
transformers:
viewimportexport
RNASingleProfileHmmDirectoryFmt

ProfileHMM[MultipleProtein]

A collection of profile Hidden Markov Models, each representing a group of related proteins.

plugin: types
format: ProteinMultipleProfileHmmDirectoryFmt
transformers:

ProfileHMM[MultipleDNA]

A collection of profile Hidden Markov Models, each representing a group of related DNA sequences.

plugin: types
format: DNAMultipleProfileHmmDirectoryFmt
transformers:
viewimportexport
DNAMultipleProfileHmmDirectoryFmt

ProfileHMM[MultipleRNA]

A collection of profile Hidden Markov Models, each representing a group of related RNA sequences.

plugin: types
format: RNAMultipleProfileHmmDirectoryFmt
transformers:
viewimportexport
RNAMultipleProfileHmmDirectoryFmt

ReferenceDB[Eggnog]

plugin: types
format: EggnogRefDirFmt
transformers:
viewimportexport
EggnogRefDirFmt

ReferenceDB[Diamond]

plugin: types
format: DiamondDatabaseDirFmt
transformers:

ReferenceDB[NCBITaxonomy]

plugin: types
format: NCBITaxonomyDirFmt
transformers:
viewimportexport
NCBITaxonomyDirFmt

ReferenceDB[EggnogProteinSequences]

plugin: types
format: EggnogProteinSequencesDirFmt
transformers:
viewimportexport
EggnogProteinSequencesDirFmt

SampleData[AlphaDiversity]

Alpha diversity values, each associated with a single sample identifier.

plugin: types
format: AlphaDiversityDirectoryFormat
transformers:

Phylogeny[Unrooted]

A phylogenetic tree not containing a defined root.

plugin: types
format: NewickDirectoryFormat
transformers:
viewimportexport
NewickFormat
NewickDirectoryFormat

Phylogeny[Rooted]

A phylogenetic tree containing a defined root.

plugin: types
format: NewickDirectoryFormat
transformers:
viewimportexport
NewickFormat
NewickDirectoryFormat

Hierarchy

plugin: types
format: NewickDirectoryFormat
transformers:
viewimportexport
NewickFormat
NewickDirectoryFormat

Dist1D[Multi, Matched]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[Multi, Independent]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[Ordered, Matched]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[NestedOrdered, Independent]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[NestedUnordered, Matched]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[Unordered, Matched]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[Ordered, Independent]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[NestedUnordered, Independent]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[Unordered, Independent]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

Dist1D[NestedOrdered, Matched]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat

StatsTable[Pairwise]

plugin: types
format: TableJSONLDirFmt
transformers:
viewimportexport
TableJSONLDirFmt
TableJSONLFileFormat