Whole Genome Sequence Classifiers#

biolockj.module.classifier.wgs is a sub-package of module.classifier.

Package modules categorize whole genome sequence micbrobial samples into Operational Taxonomic Units (OTUs) either by reference or with clustering algorithms.

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Humann2Classifier#

#BioModule biolockj.module.classifier.wgs.Humann2Classifier

Description: Use the Biobakery HumanN2 program to generate the HMP Unified Metabolic Analysis Network.

Options:

• humann2.disablePathAbundance
• humann2.disablePathCoverage
• humann2.disableGeneFamilies
• humann2.nuclDB
• humann2.protDB

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KrakenClassifier#

#BioModule biolockj.module.classifier.wgs.KrakenClassifier

Description: Classify WGS samples with KRAKEN.

Options:

• kraken.db

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Kraken2Classifier#

#BioModule biolockj.module.classifier.wgs.Kraken2Classifier

Description: Classify WGS samples with KRAKEN 2.

Options:

• kraken2.db

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Metaphlan2Classifier#

#BioModule biolockj.module.classifier.wgs.Metaphlan2Classifier

Description: Classify WGS samples with MetaPhlAn.

Options:

• exe.python
• metaphlan2.db
• metaphlan2.mpa_pkl

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