- KNEAD_DBS - Static variable in class biolockj.module.seq.KneadData
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Config required property to the contaminent databases "kneaddata.dbs":
- KneadData - Class in biolockj.module.seq
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This BioModule runs biobakery kneaddata program to remove contaminated DNA.
Multiple contaminent DNA databases can be used to filter reads simultaniously.
Common contaminents include Human, Viral, and Plasmid DNA.
- KneadData() - Constructor for class biolockj.module.seq.KneadData
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- Kraken2Classifier - Class in biolockj.module.classifier.wgs
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This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format.
- Kraken2Classifier() - Constructor for class biolockj.module.classifier.wgs.Kraken2Classifier
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- Kraken2Node - Class in biolockj.node.wgs
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- Kraken2Node(String, String) - Constructor for class biolockj.node.wgs.Kraken2Node
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Build the OtuNode by extracting the OTU names for each level from the line.
- Kraken2Parser - Class in biolockj.module.implicit.parser.wgs
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This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
- Kraken2Parser() - Constructor for class biolockj.module.implicit.parser.wgs.Kraken2Parser
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- KRAKEN_DATABASE - Static variable in class biolockj.module.classifier.wgs.Kraken2Classifier
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Config property must contain file path to Kraken kmer database directory:
"kraken2.db"
- KRAKEN_DATABASE - Static variable in class biolockj.module.classifier.wgs.KrakenClassifier
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Config property must contain file path to Kraken kmer database directory:
"kraken.db"
- KRAKEN_FILE - Static variable in class biolockj.module.classifier.wgs.Kraken2Classifier
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File suffix added by BioLockJ to kraken output files (before translation): "_kraken2_out.txt"
- KRAKEN_FILE - Static variable in class biolockj.module.classifier.wgs.KrakenClassifier
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File suffix added by BioLockJ to kraken output files (before translation): "_kraken_out.txt"
- KrakenClassifier - Class in biolockj.module.classifier.wgs
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This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format.
- KrakenClassifier() - Constructor for class biolockj.module.classifier.wgs.KrakenClassifier
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- KrakenNode - Class in biolockj.node.wgs
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- KrakenNode(String, String) - Constructor for class biolockj.node.wgs.KrakenNode
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Constructor called for each line of Kraken output.
Builds the OtuNode by extracting the OTU names for each taxonomy level found in the line.
- KrakenParser - Class in biolockj.module.implicit.parser.wgs
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This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
- KrakenParser() - Constructor for class biolockj.module.implicit.parser.wgs.KrakenParser
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