| Class | Description |
|---|---|
| PanAAddPosToTagMapPlugin |
Add alignment information from Bowtie2 to tagMap. Used to identify unique ref tags for model training
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| PanABuildPivotTBTPlugin |
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
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| PanABuildTagBlockPosPlugin |
Build blocked physical position of tags. The blocked physical position of tag is used to block the corresponding marker in genetic mapping if the tag is mapping to the marker coming from itself Positions come from TOPM alignment hypothesis or the best position from machine learning prediction
|
| PanABuildTagGWASMapPlugin |
Convert mapping result to HDF5
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| PanABuildTrainingSetPlugin |
Build training data set from tagMap, including boxcox transformation and converting to ARFF format
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| PanAFilteringTagMapPlugin |
Filtering high quality mapped tag and write them into a file, based on the predicted distance
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| PanAH5ToAnchorPlugin |
Reformat HDF5 genotype to
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| PanAMergeMappingResultPlugin |
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
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| PanAModelTrainingPlugin |
Training data with M5Rules model, generate model file and training report files
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| PanAPredictionPlugin |
Make predictions based on trained machine learning model. Write predicted values into tagMap file
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| PanAReadDigestPlugin |
Digest Fastq/Qseq data with recognition sequence Do not use underscore in taxa name in keyfile
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| PanAReadToKmerPlugin |
Generate Kmers from Fastq/Qseq data Do not use underscore in taxa name in keyfile
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| PanASamToMultiPositionTOPMPlugin |
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
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| PanASplitTBTPlugin |
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
|
| PanASplitTagBlockPosPlugin |
Split TagBlockPos
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| PanATagGWASMappingPlugin |
Genetic mapping (GWAS) tags
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| PanATagMapToFastaPlugin |
Output sequence in tagMap (e.g.
|
| PanAUsageExample |