module.classifier.r16s - RCChan5/BioLockJ GitHub Wiki

biolockj.module.classifier.r16s is a sub-package of module.classifier.

Package modules extend ClassifierModuleImpl to cluster and classify 16S micbrobial samples for taxonomy assignment.

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#BioModule biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Description: This module picks OTUs using a closed reference database and constructs an OTU table via the QIIME script pick_closed_reference_otus.py. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. This is the fastest OTU picking method since samples can be processed in parallel batches. Before the QIIME script is run, batches are prepared in the temp directory, with each batch directory containing a fasta directory with script.batchSize fasta files and a QIIME mapping file, created with awk, called batchMapping.tsv for the batch of samples. Inherits from QiimeClassifier.

Options:

• exe.awk

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#BioModule biolockj.module.classifier.r16s.QiimeDeNovoClassifier

Description: This module runs the QIIME pick_de_novo_otus.py script on all fasta sequence files in a single script since OTUs are assigned by a clustering algorithm. Additional parameters for this script are set using exe.classifierParams. If qiime.removeChimeras = "Y", vsearch is used to find chimeric sequences in the output and the QIIME script filter_otus_from_otu_table.py is run to remove them from ./output/otu_table.biom. Inherits from QiimeClassifier.

Options:

• exe.vsearch
• exe.vsearchParams
• qiime.removeChimeras

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#BioModule biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Description: This module runs the QIIME pick_open_reference_otus.py script on all fasta sequence files in a single script since clusters not identified in the reference database are assigned by a clustering algorithm. Additional parameters for this script are set using exe.classifierParams. If qiime.removeChimeras = "Y", vsearch is used to find chimeric sequences in the output and the QIIME script filter_otus_from_otu_table.py is run to remove them from ./output/otu_table.biom. Inherits from QiimeClassifier.

Options:

• exe.vsearch
• exe.vsearchParams
• qiime.removeChimeras

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#BioModule biolockj.module.classifier.r16s.RdpClassifier

Description: Classify 16s samples with RDP.

Options:

• exe.java
• rdp.db
• rdp.jar
• rdp.minThresholdScore

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See also: Typical QIIME Pipeline