OTU report modules#

Modules in the biolockj.module.report sub-pakcage normalize ParserModule output, merge the OTU tables with the metadata, or process OTU tables.

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CompileOtuCounts#

#BioModule biolockj.module.report.otu.CompileOtuCounts

Description: Compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.

Options:

none

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RarefyOtuCounts#

#BioModule biolockj.module.report.otu.RarefyOtuCounts

Description: Applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.

Options:

• rarefyOtuCounts.iterations
• rarefyOtuCounts.lowAbundantCutoff
• rarefyOtuCounts.quantile
• rarefyOtuCounts.removeSamplesBelowQuantile

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RemoveLowOtuCounts#

#BioModule biolockj.module.report.otu.RemoveLowOtuCounts

Description: Removes OTUs with counts below report.minCount.

Options:

• report.minCount
• report.numHits

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RemoveScarceOtuCounts#

#BioModule biolockj.module.report.otu.RemoveScarceOtuCounts

Description: Removes OTUs that are not found in enough samples.

Options:

• report.scarceCountCutoff

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