App Catalog
Run the JGI RQCFilter pipeline (BBTools v38.22)
Runs the JGI reads data preprocessing pipeline
Correct Reads with Lighter - v1.1.2
Correct errors in whole genome sequencing reads from Illumina platforms
Filter Out Low-Complexity Reads with PRINSEQ - v0.20.4
Filter out low-complexity paired- or single-end reads with PRINSEQ.
Add Insert Length to Reads Libraries - v1.2.2
Add insert length and standard deviation to paired-end ReadsLibraries objects.
Merge Reads Libraries - v1.2.2
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
Randomly Subsample Reads - v1.2.2
Split a reads library into a set of randomly subsampled reads libraries.
Translate Reads Libraries' Quality Scores - v1.2.2
Allows users to translate reads libraries' quality scores from phred64 to phred33.
Merge Multiple ReadsSets into One ReadsSet - v1.7.6
Use this App to merge multiple ReadsSets into one consolidated ReadsSet.
BFC - Bloom Filter Read Error Correction
Error correction for short illumina reads
Cutadapt - v1.18
Removes the 3' or 5' adapters from reads using cutadapt.
Compute Simple Read Library Stats
Run the EA Utils program fastq-stats to compute and print basic summary stats.
Join Overlapping Mate Pairs with ea-utils FASTQ-JOIN
Run the ea-utils program fastq-join to join overlapping mate pairs.
Assess Read Quality with FastQC - v0.12.1
A quality control application for high throughput sequence data.
Assess Reads Quality with NanoPlot
Generate quality assessment graphs for Oxford Nanopore reads.
Trim Reads with Trimmomatic - v0.39
Trim paired- or single-end Illumina reads with Trimmomatic.
Import SRA File as Reads From Web - v1.0.10
Import an SRA file from a web URL into your Narrative as a Reads data object.
Import Paired-End Reads from Web - v1.0.12
Import a Paired-End Library into your Narrative as a Reads object.
Import Single-End Reads from Web - v1.0.12
Import a Single-End Library into your Narrative as a Reads object.
Create Up/Down Regulated FeatureSet and ExpressionMatrix
Create up/down regulated FeatureSet and ExpressionMatrix from differential expression data based on given cutoffs.
Assemble Reads with MEGAHIT v1.2.9
Assemble metagenomic reads using the MEGAHIT assembler.
Modify Bins in BinnedContigs - v1.0.2
Add or remove specific bins by name in BinnedContigs data
Extract Bins as Assemblies from BinnedContigs - v1.0.2
Extract a bin as an Assembly from a BinnedContig dataset
Fractionate Contigs - v1.2.0
Separate Contigs in Assembly objects by presence/absence with respect to another object
Assemble Reads with IDBA-UD - v1.1.3
Assemble paired-end reads from single-cell or metagenomic sequencing technologies using the IDBA-UD assembler.
Assess Genome Quality with CheckM - v1.0.18
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
Filter Bins by Quality with CheckM - v1.0.18
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
Assemble Reads with HybridSPAdes - v3.15.3
Assemble reads using the HybridSPAdes assembler.
Assemble Reads with metaSPAdes - v3.15.3
Assemble metagenomic reads using the SPAdes assembler.
Batch Create Assembly Set - v1.2.0
Allows user to create an AssemblySet without specifying names
Compare Assembled Contig Distributions - v1.1.2
View distributions of contig characteristics for different assemblies.
Bin Contigs using CONCOCT - v1.1
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq read alignments using Cufflinks.
Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
Bin Contigs using MaxBin2 - v2.2.4
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
Assess Quality of Assemblies with QUAST - v4.4
Run QUAST (QUality ASsessment Tool) on a set of Assemblies to assess their quality.
Assemble Transcripts using StringTie - v2.1.5
Assemble the transcripts from RNA-seq read alignments using StringTie.
Batch Import Assembly from Staging Area
Import FASTA files from your staging area into your Narrative as Assembly data object
Annotate Domains in a Genome - v1.0.10
Annotate a Genome object with protein domains from widely used domain libraries.
Compare Metabolic Annotations
Conduct a side-by-side comparison of various metabolic annotations mapped into a genome
Import Annotations from Staging
Import a file in TSV format from your staging area with new annotations to add to an existing genome
Bulk Import Annotations from Staging
Import a file in TSV format from your staging area with new annotations to add to an existing genome
Merge Metabolic Annotations
Merge multiple metabolic annotations into a single merged annotation based on thresholds
Annotate Assembly and Re-annotate Genomes with Prokka - v1.14.5
Annotate Assembly and Re-annotate Genomes with Prokka annotation pipeline.
Annotate Metagenome Assembly with Prokka - v1.14.5
Annotate Metagenome Assembly with Prokka annotation pipeline.
Annotate Microbial Assembly with RASTtk - v1.073
Annotate a bacterial or archaeal assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Annotate Multiple Microbial Assemblies with RASTtk - v1.073
Annotate bacterial or archaeal assemblies and/or assembly sets using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Annotate Genome/Assembly with RASTtk - v1.073
Annotate or re-annotate genome/assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Annotate Metagenome Assembly and Re-annotate Metagenome with RASTtk - v1.073
Annotate Metagenome Assembly and Re-annotate Metagenome with RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Bulk Annotate Genomes/Assemblies with RASTtk - v1.073
Annotate or re-annotate genomes/assemblies using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Annotate Microbial Genome with RASTtk - v1.073
Annotate or re-annotate bacterial or archaeal genome using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Annotate Multiple Microbial Genomes with RASTtk - v1.073
Annotate or re-annotate bacterial or archaeal genomes and/or genome sets using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
Annotate with Snekmer Apply
Annotate Genome or Protein Sequence Set Object with Snekmer Apply.
Annotate and Distill Assemblies with DRAM
Annotate your assemblies, isolate genomes, or MAGs with DRAM and distill resulting annotations to create an interactive functional summary per genome or assembly. Use for KBase assembly objects.
Annotate and Distill Genomes with DRAM
Annotate MAGs with DRAM and distill resulting annotations to create an interactive functional summary per genome. Use for KBase genome objects.
Annotate and Distill Viral Assemblies with DRAM-v
Annotate vMAGs with DRAM and distill resulting annotations to create an interactive auxiliary metabolic gene summary. Use with the VirSorter KBase app.
Batch Create Assembly Set - v1.2.0
Allows user to create an AssemblySet without specifying names
Search with HMMs of MicroTrait Bioelement families - v1
Search for matches to HMMs of MicroTrait environmental bioelement cycling families using HMMER 3
Search with HMMs of Phylogenetic Marker families - v1
Search for matches to Bacterial and Archaeal Phylogenetic Marker families using HMMER 3
Search with dbCAN2 HMMs of CAZy families - v10
Search for matches to dbCAN HMMs of CAZy carbohydrate active enzyme families using HMMER 3
Annotate Plant Enzymes with OrthoFinder
Annotates transcripts in a Genome object with metabolic functions using OrthoFinder.
Annotate Domains in a GenomeSet - v1.7.1
Annotate domains in every Genome within a GenomeSet using protein domains from widely used domain libraries.
Annotate Plant Transcripts with Metabolic Functions
Annotating transcripts with metabolic functions
Batch Import Genome from Staging Area
Import files (GenBank or GFF + FASTA) from your staging area into your Narrative as a Genome data object
Curated Blast (M Price)
Run Morgan Price's program, "Curated Blast", on a Genome in KBase.
Align Reads using Bowtie2 - v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
Join Multiple Sequence Alignments (MSAs) - v1.3.0
Allows user to concatenate two (or more) MSAs
Assess Reads Alignment Quality using Qualimap - v2.2.1
Display BAM quality control information for a ReadsAlignment or ReadsAlignmentSet using QualiMap.
BLASTn nuc-nuc Search - v2.13.0+
Search for untranslated feature matches to a nucleotide query sequence.
BLASTp prot-prot Search - v2.13.0+
Search for protein matches to an input protein sequence.
BLASTx nuc-prot Search - v2.13.0+
Search for protein matches to an input nucleotide sequence.
GBLOCKS Trim Multiple Sequence Alignment (MSA) - v0.91b
Trim a Multiple Sequence Alignment (MSA) to remove hypervariable (gappy) regions with Gblocks
Align Reads using HISAT2 - v2.1.0
Align sequencing reads to long reference sequences using HISAT2.
HMMER Custom Search & Functional Profile - v3.3.2
Search for matches to all MSAs that are within workspace using Hidden Markov Model (HMMER) Search.
HMMER Search from MSA (prot-prot) - v3.3.2
Search for matches to a Multiple Sequence Alignment (MSA) using Hidden Markov Model Search (hmmsearch).
Search with HMMs of MicroTrait Bioelement families - v1
Search for matches to HMMs of MicroTrait environmental bioelement cycling families using HMMER 3
Search with HMMs of Phylogenetic Marker families - v1
Search for matches to Bacterial and Archaeal Phylogenetic Marker families using HMMER 3
Search with dbCAN2 HMMs of CAZy families - v10
Search for matches to dbCAN HMMs of CAZy carbohydrate active enzyme families using HMMER 3
MUSCLE Multiple Sequence Alignment (DNA) - v3.8.425
Build a Multiple Sequence Alignment (MSA) for nucleotide sequences using MUSCLE.
MUSCLE Multiple Sequence Alignment (Protein) - v3.8.425
Build a Multiple Sequence Alignment (MSA) for protein sequences using MUSCLE.
Run PaperBLAST on a Protein Sequence
Find papers related to a protein sequence with PaperBLAST.
Align Reads using TopHat2 - v1.0.1
Align sequencing reads to a reference genome using TopHat2 to identify exon-exon splice junctions.
Compute ANI with FastANI
Allows users to compute fast whole-genome Average Nucleotide Identity (ANI) estimation.
Build FeatureSet from Genome
Create a new FeatureSet by selecting features from a Genome.
Compare Genomes from Pangenome
Compare isofunctional and homologous gene families for all genomes in a Pangenome.
Compare Two Proteomes
Compute bi-directional-best-hits between the proteins present in two input Genomes. Produces a dot plot matrix showing corresponding genes in two Genomes, as well as a table of gene differences.
Build Pangenome with OrthoMCL - v2.0
Create a Pangenome object by performing OrthoMCL orthologous groups construction on a set of Genomes.
Build GenomeSet From Tree
Allows users to extract a set of genomes (GenomeSet data object) from a SpecieTree.
Insert Set of Genomes Into SpeciesTree - v2.2.0
Add a user-provided GenomeSet to a KBase SpeciesTree.
Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
Propagate Model to New Genome
Translate the metabolic model of one organism to another, using a mapping of similar proteins between their genomes.
Join Multiple Sequence Alignments (MSAs) - v1.3.0
Allows user to concatenate two (or more) MSAs
Batch Create Genome Set - v1.2.0
Allows user to create a GenomeSet without specifying names
Build GenomeSet from FeatureSet - v1.7.6
Allows users to extract a GenomeSet from a FeatureSet.
Venn Slice Two AssemblySets - v1.7.6
Allows users to slice two AssemblySets according to their Venn overlap.
Venn Slice Two FeatureSets - v1.7.6
Allows users to slice two FeatureSets according to their Venn overlap.
Venn Slice Two GenomeSets - v1.7.6
Allows users to slice two GenomeSets according to their Venn overlap.
Merge FeatureSets - v1.7.4
Use this App to combine multiple FeatureSets into a single consolidated set.
Merge GenomeSets - v1.7.4
Use this App to combine multiple GenomeSets into a single consolidated set.
Slice FeatureSets by Genomes - v1.8.0
Allows user to slice FeatureSets by Genomes and/or Metagenomes.
Find Gene Set Interconnectivity using Cross Validation with RWRtools CV
RWRtools CV (Cross Validation) performs cross validation on a single gene set, finding the RWR rank of the left-out genes.
Find Functional Context using Lines of Evidence with RWRtools LOE
RWRtools LOE (Lines of Evidence) uses RWR to rank genes in the network starting from a Feature Set.
Build Phylogenetic Tree from MSA using FastTree2 - v2.1.11
Build a phylogenetic reconstruction from a Multiple Sequence Alignment (MSA) using FastTree2.
Functional Enrichment for GO Terms - v1.0.8
Compute gene ontology (GO) term enrichment for genomic features.
GBLOCKS Trim Multiple Sequence Alignment (MSA) - v0.91b
Trim a Multiple Sequence Alignment (MSA) to remove hypervariable (gappy) regions with Gblocks
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
Calculate Pangenome with mOTUpan - v0.3.2
Calculate pangenome for microbial genomes, including MAGs of varying quality
MUSCLE Multiple Sequence Alignment (DNA) - v3.8.425
Build a Multiple Sequence Alignment (MSA) for nucleotide sequences using MUSCLE.
MUSCLE Multiple Sequence Alignment (Protein) - v3.8.425
Build a Multiple Sequence Alignment (MSA) for protein sequences using MUSCLE.
Build Gene Tree - v1.7.1
Build Gene Tree for a set of homologously related genes in a FeatureSet
Build Microbial SpeciesTree - v1.6.0
Build Species Tree for your Microbial Genomes, optionally including Tree Skeleton of Phylum Exemplars
Homolog Genome Context - v1.5.1
Find Homologs for a Collection of Genes and View in Genome Context
Annotate Domains in a GenomeSet - v1.7.1
Annotate domains in every Genome within a GenomeSet using protein domains from widely used domain libraries.
Score Orthologs Evolutionary Rates - v1.9.0
Score the evolutionary rates of orthologs and save most conserved and most divergent features
Trim SpeciesTree to GenomeSet- v1.6.0
Allows users to reduce a SpeciesTree to match the genomes in a GenomeSet.
View Function Profile for Genomes - v1.6.0
Examine the general functional distribution or specific functional gene families for a GenomeSet.
View Function Profile for FeatureSet - v1.8.0
Examine the general functional distribution or specific functional gene families for a given FeatureSet.
View Function Profile for a Phylogenetic Tree - v1.6.0
Examine the distribution of functional gene families for organisms in a phylogenetic SpeciesTree.
Compare Metabolic Annotations
Conduct a side-by-side comparison of various metabolic annotations mapped into a genome
Import Annotations from Staging
Import a file in TSV format from your staging area with new annotations to add to an existing genome
Bulk Import Annotations from Staging
Import a file in TSV format from your staging area with new annotations to add to an existing genome
Merge Metabolic Annotations
Merge multiple metabolic annotations into a single merged annotation based on thresholds
MS2 - Build Prokaryotic Metabolic Models with OMEGGA
Using ModelSEED2 pipeline, construct draft metabolic models based on input annotated genomes.
MS2 - Improved Gapfill Metabolic Models with OMEGGA
Identify the minimal set of biochemical reactions to add to draft metabolic models to enable them to produce a desired flux in a specified media.
Run Flux Mutual Information Analysis
Explore the mutual information between model flux and media inputs
Build Metabolic Model
Construct a draft metabolic model based on an annotated genome.<b>This app is now obsolete, replaced by the new ModelSEED2 app: <i>MS2 - Build Prokaryotic Metabolic Models</i>.</b>
Build Metagenome Metabolic Model (v0.1)
Generate a draft metabolic model based on an annotated genome.
Build Multiple Metabolic Models
Construct draft metabolic models based on annotated genomes.
Compare FBA Solutions
For each flux balance analysis (FBA) solution, compare objective values, reaction fluxes, and metabolite uptake and excretion.
Compare Flux with Expression
Compare reaction fluxes with gene expression values to identify metabolic pathways where expression and flux data agree or conflict.
Compare Models
This App compares Flux Balance Analysis (FBA) models based on reactions, compounds, biomass, and protein families.
Edit Metabolic Model
Edit a metabolic model by adding, removing, or altering compounds, reactions, or biomass formulations.
Fit Model to Exometabolite Data
Identify the minimal set of biochemical reactions to add to a draft metabolic model to enable production and consumption of as many exometabolites as possible
Gapfill Metabolic Model
Identify the minimal set of biochemical reactions to add to a draft metabolic model to enable it to produce biomass in a specified media.<b>This app is now obsolete, replaced by the new ModelSEED2 app: <i>MS2 - Improved Gapfill Metabolic Models</i>.</b>
Merge Metabolic Models into Community Model
Merge two or more metabolic models into a compartmentalized community model.
Propagate Model to New Genome
Translate the metabolic model of one organism to another, using a mapping of similar proteins between their genomes.
Run Flux Balance Analysis
Predict metabolite fluxes in a metabolic model of an organism grown on a given media using flux balance analysis (FBA).
Run Model Characterization
Runs a variety of algorithms on a model to characterize its quality, pathways, and auxotrophy.
Simulate Growth on Phenotype Data
Use flux balance analysis (FBA) to simulate multiple growth phenotypes.
Import JSON File as EscherMap from Staging Area
Import a JSON file from your staging area into your Narrative as an KBaseFBA.EscherMap data object
Integrate Abundances with Metabolism
Integrate gene abundances with a plant primary metabolic network
Reconstruct Plant Metabolism
Reconstruct the metabolic network of a plant based on an annotated genome.
Cluster Expression Data - WGCNA
Perform weighted gene co-expression network analysis (WGCNA) to detect gene clusters and expression patterns.
Filter Expression Matrix
Filter an expression matrix using either Log Odds Ratio (LOR) or ANalysis of VAriance (ANOVA) algorithms.
View Multi-cluster Heatmap
Explore an expression matrix as a multi-cluster heatmap of gene expression levels.
View P-value Distribution for Differential Expression
Display the P-value distribution of differentially expressed genes to filter an expression matrix based on P-value cutoff or number of features.
Create Average ExpressionMatrix
Create an average ExpressionMatrix data object with one column per condition.
Filter ExpressionMatrix with FeatureSet
Create a subset of gene expression values including only genes, which match genes provided in a list.
Create Up/Down Regulated FeatureSet and ExpressionMatrix
Create up/down regulated FeatureSet and ExpressionMatrix from differential expression data based on given cutoffs.
Cluster Expression Data - Hierarchical
Perform hierarchical clustering to group gene expression data into a dendrogram.
Cluster Expression Data - K-Means
Perform K-means clustering to group expression data for observing and analyzing patterns of gene expression.
Reconstruct Hierarchical Clusters
Produce new hierarchical clusters from existing ones based on a new tree cutoff parameter.
Estimate K for K-Means Clustering
Compute reasonable values of K for use in K-means clustering.
Associate Expression Matrix to Genome Features
Associate an ExpressionMatrix with an annotated Genome that contains features referenced in the matrix.
Impute Missing Expression Values in ExpressionMatrix - v1.0
Replace missing expression values in an ExpressionMatrix with the average of all other values present in a given row.
View Expression Matrix Heatmap In Feature Table
Explore an Expression Matrix as a sortable heatmap of selected features.
View Expression Matrix Heatmap in Condition Table
Explore an Expression Matrix by viewing a sortable heatmap of selected conditions.
View Pairwise Correlation for Expression Data
Explore pairwise correlation values of selected features as a heatmap.
View Expression Profile
Explore the expression profile of an Expression Matrix.
View Sample Properties 2D Plot
View 2D plot of samples for a selected pair of properties
View Sample Properties Bar Chart
View bar chart of all property values for a selected set of samples from SamplePropertyMatrix
Create RNA-seq SampleSet
Allows users to provide RNA-seq reads and the corresponding metadata to create an RNASeqSampleSet data object.
Create RNA-seq SampleSet With Condition Set
Provide RNA-seq reads and the metadata to create an RNA-seq Sample Set
Compare Flux with Expression
Compare reaction fluxes with gene expression values to identify metabolic pathways where expression and flux data agree or conflict.
Align Reads using Bowtie2 - v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2.
Assess Reads Alignment Quality using Qualimap - v2.2.1
Display BAM quality control information for a ReadsAlignment or ReadsAlignmentSet using QualiMap.
Create Differential Expression Matrix using Ballgown - v3.5
Create differential expression matrix based on a given threshold cutoff (for eukaryotes only)
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq read alignments using Cufflinks.
Create Differential Expression using Cuffdiff - v2.2.1
Identify differential expression in the gene and transcript expression level using Cuffdiff.
Create Differential Expression Matrix using DESeq2 - v1.20.0
Create differential expression matrix based on a given threshold cutoff
Functional Enrichment for GO Terms - v1.0.8
Compute gene ontology (GO) term enrichment for genomic features.
Align Reads using HISAT2 - v2.1.0
Align sequencing reads to long reference sequences using HISAT2.
Assemble Transcripts using StringTie - v2.1.5
Assemble the transcripts from RNA-seq read alignments using StringTie.
Align Reads using TopHat2 - v1.0.1
Align sequencing reads to a reference genome using TopHat2 to identify exon-exon splice junctions.
Run Fama Read Profiling - v1.1
Generate a functional profile of sequence read libraries with Fama
Assemble Reads with MEGAHIT v1.2.9
Assemble metagenomic reads using the MEGAHIT assembler.
Modify Bins in BinnedContigs - v1.0.2
Add or remove specific bins by name in BinnedContigs data
Extract Bins as Assemblies from BinnedContigs - v1.0.2
Extract a bin as an Assembly from a BinnedContig dataset
Annotate Metagenome Assembly with Prokka - v1.14.5
Annotate Metagenome Assembly with Prokka annotation pipeline.
Merge Metabolic Models into Community Model
Merge two or more metabolic models into a compartmentalized community model.
Classify Taxonomy of Metagenomic Reads with GOTTCHA2 - v2.1.7
Uses GOTTCHA2 to provide taxonomic classifications of shotgun metagenomic reads data.
Assemble Reads with IDBA-UD - v1.1.3
Assemble paired-end reads from single-cell or metagenomic sequencing technologies using the IDBA-UD assembler.
Assess Genome Quality with CheckM - v1.0.18
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
Filter Bins by Quality with CheckM - v1.0.18
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes. Creates a new BinnedContigs object with High Quality bins that pass user-defined thresholds for Completeness and Contamination.
Assemble Reads with metaSPAdes - v3.15.3
Assemble metagenomic reads using the SPAdes assembler.
Find Strain Genomes with StrainFinder v1
Runs the StrainFinder v1 method to obtain haplotype modes
Compare Assembled Contig Distributions - v1.1.2
View distributions of contig characteristics for different assemblies.
Bin Contigs using CONCOCT - v1.1
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
Classify Taxonomy of Metagenomic Reads with Kaiju - v1.9.0
Allows users to perform taxonomic classification of shotgun metagenomic read data with Kaiju.
Bin Contigs using MaxBin2 - v2.2.4
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
Call Microbial SNPs
Call Microbial SNPs relative to a reference sequence, using BCFtools mpileup
Calculate Pangenome with mOTUpan - v0.3.2
Calculate pangenome for microbial genomes, including MAGs of varying quality
Build FeatureSet from Genome
Create a new FeatureSet by selecting features from a Genome.
Create Chemical Abundance Matrix Template
Create a template file for Import Chemical Abundance Matrix app
Compute Correlation Matrix
Create a KBaseExperiments. CorrelationMatrix with KBaseMatrices object
Compute Correlation Matrix Between Two Matrices
Compute Correlation Matrix Between Two Matrices
Perform Mantel Test Analysis
Compute correlation between distance matrices using the Mantel test
Perform Similarity Percentage (SIMPER) Statistics Analysis
Perform Similarity Percentage (SIMPER) Statistics Analysis
Perform Categorical Variable Statistics Analysis
Perform Categorical Variable Statistics Analysis on a Matrix object
Transform Matrix
Performaing Standardization/Ratio Transformation Algorithm from input matrix
Transform Selected Variables From Matrix
Performaing Standardization/Ratio Transformation Algorithm from input matrix on selected Variables
View Sample Properties 2D Plot
View 2D plot of samples for a selected pair of properties
View Sample Properties Bar Chart
View bar chart of all property values for a selected set of samples from SamplePropertyMatrix
Taxonomy Abundance Barplot
Create a relative abundance bar chart at all main taxonomic ranks, along with optional grouping of bars based on sample metadata.
Fractionate Contigs - v1.2.0
Separate Contigs in Assembly objects by presence/absence with respect to another object
FeatureSet/SequenceSet Object Info
Create text info files based on a FeatureSet or a SequenceSet
Multiple Sequence Alignment Object Info
Create text info files based on a Multiple Sequence Alignment data object
Proteome Comparison Object Info
Create text info files based on a Proteome Comparison data object
Join Multiple Sequence Alignments (MSAs) - v1.3.0
Allows user to concatenate two (or more) MSAs
Update Genome Species Name - v1.1.0
Allows user to add/change the Scientific Name field of Genome objects
Add Insert Length to Reads Libraries - v1.2.2
Add insert length and standard deviation to paired-end ReadsLibraries objects.
Merge Reads Libraries - v1.2.2
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
Randomly Subsample Reads - v1.2.2
Split a reads library into a set of randomly subsampled reads libraries.
Translate Reads Libraries' Quality Scores - v1.2.2
Allows users to translate reads libraries' quality scores from phred64 to phred33.
Batch Create Assembly Set - v1.2.0
Allows user to create an AssemblySet without specifying names
Batch Create Genome Set - v1.2.0
Allows user to create a GenomeSet without specifying names
Build GenomeSet from FeatureSet - v1.7.6
Allows users to extract a GenomeSet from a FeatureSet.
Venn Slice Two AssemblySets - v1.7.6
Allows users to slice two AssemblySets according to their Venn overlap.
Venn Slice Two FeatureSets - v1.7.6
Allows users to slice two FeatureSets according to their Venn overlap.
Venn Slice Two GenomeSets - v1.7.6
Allows users to slice two GenomeSets according to their Venn overlap.
Merge FeatureSets - v1.7.4
Use this App to combine multiple FeatureSets into a single consolidated set.
Merge GenomeSets - v1.7.4
Use this App to combine multiple GenomeSets into a single consolidated set.
Merge Multiple ReadsSets into One ReadsSet - v1.7.6
Use this App to merge multiple ReadsSets into one consolidated ReadsSet.
Slice FeatureSets by Genomes - v1.8.0
Allows user to slice FeatureSets by Genomes and/or Metagenomes.
Compare Assembled Contig Distributions - v1.1.2
View distributions of contig characteristics for different assemblies.
Export Object JSON To Staging Area
Export a KBase object's JSON represenation to the Staging Area.
Export Data Object To Staging Area
Export files associated with a Reads, Genome, Assembly, Annotated Metagenome Assembly, Alignment or SampleSet object to the Staging Area.
Unpack a Compressed File in Staging Area - v1.0.12
Unpack a compressed file in the staging area.
Upload File to Staging from Web - v1.0.12
Upload a data file (which may be compressed) from a web URL to your staging area.
