Package | Description |
---|---|
biolockj.module | |
biolockj.module.assembly | |
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.diversity | |
biolockj.module.diy | |
biolockj.module.getData.sra | |
biolockj.module.hello_world | |
biolockj.module.implicit |
The modules in this package are implicitly added to pipelines as needed.
These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y. |
biolockj.module.implicit.parser.r16s |
This package contains Parser
BioModule s 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
BioModule s that convert the WGS taxonomy reports generated by
WGS classifiers (such as Kraken, Kraken2 Metaphlan2, or Humann2) into standardized OTU abundance tables. |
biolockj.module.report |
This package contains
BioModule s that normalize OTU abundance tables output by Parser
modules, merges them with the metadata, and generates various reports and notifications. |
biolockj.module.report.otu | |
biolockj.module.report.r |
This package contains
BioModule s that build pipeline reports from the standard OTU abundance
tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files. |
biolockj.module.report.taxa | |
biolockj.module.rnaseq | |
biolockj.module.seq |
BioModule s used to prepare sequence files or update the metadata prior to classification. |
Modifier and Type | Class and Description |
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class |
Stop
Stop a pipeline.
|
Modifier and Type | Class and Description |
---|---|
class |
GenomeAssembly
This BioModule builds the bash scripts used to assemble WGS sequences with MetaSPAdes, bin contigs with Metabat2 and
check quality with checkM.
|
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 |
ShannonDiversity |
Modifier and Type | Class and Description |
---|---|
class |
ForEachFile |
class |
ForEachLevel
Deprecated.
|
class |
ForEachLoop |
class |
ForEachSample |
class |
GenMod
This BioModule allows users to call in their own scripts into BLJ
|
class |
Rmarkdown |
Modifier and Type | Class and Description |
---|---|
class |
SraDownload |
class |
SraMetaData |
class |
SraMetaDB |
class |
SrpSrrConverter |
Modifier and Type | Class and Description |
---|---|
class |
Hello_Friends |
class |
Hello_World |
class |
Step2
Start with the basic documentation.
|
class |
Step3
Even a very simple module probably uses at least one property.
|
class |
Step4
Specify the acceptable input data type for this module.
|
class |
Step5 |
Modifier and Type | Class and Description |
---|---|
class |
Demultiplexer
This BioModule splits multiplexed data into a separate file or pair of files (for paired reads) for each sample.
|
class |
ImportMetadata
This BioModule validates the contents/format of the project metadata file and the related Config properties.
|
Modifier and Type | Class and Description |
---|---|
class |
RdpHierParser |
class |
RdpParser
This BioModule parses RDP output files to build standard OTU abundance tables.
|
Modifier and Type | Class and Description |
---|---|
class |
Humann2Parser
This BioModule 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.
|
Modifier and Type | Class and Description |
---|---|
class |
Email
This BioModule is used to email the user the pipeline execution status and summary.
|
Modifier and Type | Class and Description |
---|---|
class |
RarefyOtuCounts
This BioModule applies a mean iterative post-OTU classification rarefication algorithm so that each output sample
will have approximately the same number of OTUs.
|
class |
RemoveLowOtuCounts
This BioModule set low OTU counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or contaminents. |
Modifier and Type | Class and Description |
---|---|
class |
R_CalculateStats
This BioModule is used to build the R script used to generate taxonomy statistics and plots.
|
class |
R_PlotEffectSize
This BioModule is used to run the R script used to generate OTU-metadata fold-change-barplots for each binary report
field.
|
class |
R_PlotMds
This BioModule is used to build the R script used to generate MDS plots for each report field and each taxonomy level
configured.
|
class |
R_PlotOtus
This BioModule is used to build the R script used to generate OTU-metadata box-plots and scatter-plots for each
report field and taxonomy level.
|
class |
R_PlotPvalHistograms
This BioModule is used to build the R script used to generate p-value histograms for each report field and each
taxonomy level configured.
|
Modifier and Type | Class and Description |
---|---|
class |
AddMetadataToTaxaTables
This BioModule is used to add metadata columns to the OTU abundance tables.
|
class |
AddPseudoCount |
class |
BuildTaxaTables
Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level.
|
class |
LogTransformTaxaTables
This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.
|
class |
NormalizeByReadsPerMillion
Normalize each sample for sequencing depth by reporting each value as the number
of counts per million counts in a given sample.
|
class |
NormalizeTaxaTables
This utility is used to normalize and/or log-transform the raw OTU counts using the formulas:
Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1
Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ]
The code implementation supports (log_base = e) and (log_base = 10) which is configured via
Constants.REPORT_LOG_BASE property. |
Modifier and Type | Class and Description |
---|---|
class |
DESeq2 |
class |
EdgeR |
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 |
Multiplexer
This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an
identifying bar-code (if defined in the metatata) is stored in the sequence header.
BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch. |
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 |
class |
RarefySeqs
This BioModule imposes a minimum and/or maximum number of reads per sample.
|
class |
SeqFileValidator
This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
|
class |
TrimPrimers
This BioModule removes sequence primers from demultiplexed files.
The primers are defined using regular expressions in a separate file. |