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.
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
KrakenClassifier#
#BioModule biolockj.module.classifier.wgs.KrakenClassifier
Description: Classify WGS samples with KRAKEN.
Options:
- kraken.db
Kraken2Classifier#
#BioModule biolockj.module.classifier.wgs.Kraken2Classifier
Description: Classify WGS samples with KRAKEN 2.
Options:
- kraken2.db
Metaphlan2Classifier#
#BioModule biolockj.module.classifier.wgs.Metaphlan2Classifier
Description: Classify WGS samples with MetaPhlAn.
Options:
- exe.python
- metaphlan2.db
- metaphlan2.mpa_pkl