| Package | Description |
|---|---|
| biolockj.module.classifier.r16s |
This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences.
Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule. |
| biolockj.module.classifier.wgs |
This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data.
As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data. Include the corresponding ParserModule in the Config file to
generate standardized OTU abundance tables. |
| biolockj.module.implicit.qiime |
This package contains
BioModules that are implicitly added to QIIME pipeline as needed. |
| Modifier and Type | Class and Description |
|---|---|
class |
QiimeClosedRefClassifier
This BioModule executes the QIIME script pick_closed_reference_otus.py on a FastA sequence files.
|
class |
QiimeDeNovoClassifier
This module runs the QIIME pick_de_novo_otus.py script on FastA sequence files in a single script so it is important
to allocate sufficient job resources if running in a clustered environment.
|
class |
QiimeOpenRefClassifier
This module runs the QIIME pick_open_reference_otus.py script on FastA sequence files in a single script so it is
important to allocate sufficient job resources if running in a clustered environment.
|
class |
RdpClassifier
This BioModule uses RDP to assign taxonomy to 16s sequences.
|
| Modifier and Type | Class and Description |
|---|---|
class |
Humann2Classifier
This BioModule runs biobakery humann2 program to generate the HMP Unified Metabolic Analysis Network
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). |
class |
Kraken2Classifier
This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format.
|
class |
KrakenClassifier
This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format.
|
class |
Metaphlan2Classifier
This BioModule builds the bash scripts used to execute metaphlan2.py to classify WGS sequences with MetaPhlAn2.
|
| Modifier and Type | Class and Description |
|---|---|
class |
QiimeClassifier
This BioModule generates the bash script used to create QIIME summary scripts, taxonomy-level reports, and add alpha
diversity metrics (if configured) to the metadata file.
For a complete list of available metrics, see: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html |