Uses of Interface
biolockj.module.implicit.parser.ParserModule

Packages that use ParserModule

Package	Description
biolockj.module.implicit.parser	This package contains Parser BioModules in the r16s and WGS sub-packages that are paired with a ClassifierModule via BioModule.getPostRequisiteModules() to run immediately after the classifier.
biolockj.module.implicit.parser.r16s	This package contains Parser BioModules that convert the 16S taxonomy reports generated by 16S classifiers (such as RDP and QIIME) into standardized OTU abundance tables.
biolockj.module.implicit.parser.wgs	This package contains Parser BioModules that convert the WGS taxonomy reports generated by WGS classifiers (such as Kraken, Kraken2 Metaphlan2, or Humann2) into standardized OTU abundance tables.

Uses of ParserModule in biolockj.module.implicit.parser

Classes in biolockj.module.implicit.parser that implement ParserModule

Modifier and Type	Class and Description
class	ParserModuleImpl Parser BioModules read ClassifierModule output to build standardized OTU count tables.

Uses of ParserModule in biolockj.module.implicit.parser.r16s

Classes in biolockj.module.implicit.parser.r16s that implement ParserModule

Modifier and Type	Class and Description
class	QiimeParser This BioModules parses QiimeClassifier output reports to build standard OTU abundance tables.
class	RdpParser This BioModule parses RDP output files to build standard OTU abundance tables.

Uses of ParserModule in biolockj.module.implicit.parser.wgs

Classes in biolockj.module.implicit.parser.wgs that implement ParserModule

Modifier and Type	Class and Description
class	Humann2Parser This BioModules parses Humann2Classifier output reports to build standard OTU abundance tables. Samples IDs are found in the column headers starting with the 2nd column. The count type depends on the HumanN2 config properties.
class	Kraken2Parser This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
class	KrakenParser This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
class	Metaphlan2Parser This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.