Uses of Class
biolockj.module.SeqModuleImpl

Packages that use SeqModuleImpl

Package	Description
biolockj.module.classifier	This package contains Classifier specific BioModules that build bash scripts to generate taxonomy reports from the sequences files.
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.
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.

Uses of SeqModuleImpl in biolockj.module.classifier

Subclasses of SeqModuleImpl in biolockj.module.classifier

Modifier and Type	Class and Description
class	ClassifierModuleImpl This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.

Uses of SeqModuleImpl in biolockj.module.classifier.r16s

Subclasses of SeqModuleImpl in biolockj.module.classifier.r16s

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.

Uses of SeqModuleImpl in biolockj.module.classifier.wgs

Subclasses of SeqModuleImpl in biolockj.module.classifier.wgs

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.

Uses of SeqModuleImpl in biolockj.module.implicit.qiime

Subclasses of SeqModuleImpl in biolockj.module.implicit.qiime

Modifier and Type	Class and Description
class	BuildQiimeMapping This BioModule converts the metadata file into a tab delimited QIIME mapping file (if provided). The QIIME mapping file is validated by calling QIIME script validate_mapping_file.py
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

Uses of SeqModuleImpl in biolockj.module.seq

Subclasses of SeqModuleImpl in biolockj.module.seq

Modifier and Type	Class and Description
class	AwkFastaConverter This BioModule uses awk and gzip to convert input sequence files into a decompressed fasta file format.
class	Gunzipper This BioModule uses gzip to decompress input sequence files.
class	KneadData This BioModule runs biobakery kneaddata program to remove contaminated DNA. Multiple contaminent DNA databases can be used to filter reads simultaniously. Common contaminents include Human, Viral, and Plasmid DNA.
class	PearMergeReads This BioModule will merge forward and reverse fastq files using PEAR. For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html