> For the complete documentation index, see [llms.txt](https://documentation.dnanexus.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://documentation.dnanexus.com/user/running-apps-and-workflows/tools-list.md).
# Tools List
## Public Tools
### Annotation Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| -------------------------------------------------------------------------------------------------------------------------- | ------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| SnpEff Annotate
snpeff\_annotate
| SnpEff | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| SnpSift Annotate
snpsift\_annotate
| SnpSift | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
### Data Transfer Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| AWS S3 Exporter
aws\_platform\_to\_s3\_file\_transfer
| AWS S3 | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| AWS S3 Importer
aws\_s3\_to\_platform\_files
| AWS S3 | All regions |
| SRA FASTQ Importer
sra\_fastq\_importer
| Retrieve reads in FASTQ format from SRA ([SRA toolkit fasterq-dump](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump)) | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### DNAseq Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Original Quality Functionally Equivalent
oqfe
| WGS, WES- alignment and duplicate marking (A revision of [Functionally Equivalent](https://www.nature.com/articles/s41467-018-06159-4)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)
gatk4\_bqsr\_parallel
| GATK4 - [BaseRecalibrator](https://gatk.broadinstitute.org/hc/en-us/articles/360046222991-BaseRecalibrator) and [ApplyBQSR](https://gatk.broadinstitute.org/hc/en-us/articles/360046222011-ApplyBQSR) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| BWA-MEM FASTQ Read Mapper
bwa\_mem\_fastq\_read\_mapper
| Short read alignment (BWA-MEM) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)
gatk4\_haplotypecaller\_parallel
| Variant calling, post-alignment QC ([GATK4- HaplotypeCaller module](https://gatk.broadinstitute.org/hc/en-us/articles/360045799892-HaplotypeCaller)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)
gatk4\_genotypegvcfs\_single\_sample\_parallel
| [GATK4- GenotypeGVCFs module](https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| Picard MarkDuplicates Mappings Deduplicator
picard\_mark\_duplicates
| Variant Calling- remove duplicates, post-alignment ([MarkDuplicates from the Picard suite of tools](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### GWAS Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| REGENIE
regenie
| REGENIE | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam, OFH-TRE (London)
|
| PLINK GWAS
plink\_gwas
| PLINK2 | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam, OFH-TRE (London)
|
| Raremetal2 - Raremetal and Raremetalworker
raremetal2
| Meta-analysis of rare variants (Raremetalworker, Raremetal) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| SAIGE GWAS - Gene and region based association tests
saige\_gwas\_gbat
| Gene and region-based association tests ([SAIGE](https://saigegit.github.io/SAIGE-doc/)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| SAIGE GWAS - Single variant association tests
saige\_gwas\_svat
| Single variant association tests ([SAIGE](https://saigegit.github.io/SAIGE-doc/)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| SAIGE GWAS GRM
saige\_gwas\_grm
| Null model fitting using a GRM for SAIGE GWAS ([SAIGE](https://saigegit.github.io/SAIGE-doc/)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| SAIGE-GWAS Sparse GRM
saige\_gwas\_sparse\_grm
| Sparse GRM construction for SAIGE GWAS ([SAIGE](https://saigegit.github.io/SAIGE-doc/)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| PLINK GWAS Pipeline
plink\_pipeline
| Plink2 | AWS: US (East), Europe (Frankfurt), Europe (London)
Azure: US (West)
|
| PLATO GWAS Pipeline
plato\_pipeline
| Plato, Plink2 | AWS: US (East), Europe (Frankfurt), Europe (London)
Azure: US (West)
|
| LocusZoom
locuszoom
| GWAS, visualization (LocusZoom) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
### File Transfer Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------- | ---------------------------------------------------- | ----------- |
| URL Fetcher
url\_fetcher
| Fetches a file from a URL onto the DNAnexus Platform | All regions |
### Imaging Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| -------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Imaging Multitool - MONAI
imaging\_multitool\_monai
| Image processing ([MONAI Core](https://github.com/Project-MONAI/MONAI)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| 3D Slicer
3d\_slicer
| Visualization and image analysis ([3D Slicer](https://github.com/Slicer/Slicer)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| 3D Slicer with MONAI Label
3d\_slicer\_monai
| Interactive radiology image analysis ([3D Slicer](https://github.com/Slicer/Slicer), [MONAI Label](https://github.com/Project-MONAI/MONAILabel/)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
### Import Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| --------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------ |
| SRA FASTQ Importer
sra\_fastq\_importer
| Retrieve reads in FASTQ format from SRA ([SRA tools: fasterq-dump](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump)) | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| URL Fetcher
url\_fetcher
| Fetches a file from a URL onto the DNAnexus Platform | All regions |
### Interactive Analysis Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Cloud Workstation
cloud\_workstation
| SSH-accessible Unix shell on a Platform cloud worker. Use it for on-demand analysis of Platform data. | All regions |
| ttyd
ttyd
| Unix shell on a Platform cloud worker in your browser. Use it for on-demand CLI operations and to launch httpsApp-enabled apps or applets on 2 extra ports | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
### Joint Genotyping Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| GLnexus
glnexus
| This app can also be used to create pVCF without running joint genotyping (GLnexus) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### Mapping Manipulation Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------- |
| SAMtools Mappings Indexer
samtools\_index
| Building BAM index file ([SAMtools](https://www.htslib.org/doc/samtools.html) - SAMtools index) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| SAMtools Mappings Sorter
samtools\_sort
| Sort alignment result based on coordinates ([SAMtools](https://www.htslib.org/doc/samtools.html) - SAMtools sort) | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### PheWAS Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------- | ------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| PHESANT
phesant
| PheWAS (PHESANT) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### PRS Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------- | -------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| PRSice 2
prsice2
| Polygenic risk scores (PRSice-2) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### QC Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| -------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| MultiQC
multiqc
| QC reporting (MultiQC) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| Qualimap2 Analysis
qualimap2\_anlys
| Qualimap2 | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| RNASeQC
rnaseqc
| Transcriptomics Expression Quantification ([RNASeQC 2](https://github.com/getzlab/rnaseqc)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| FastQC Reads Quality Control
fastqc
| FastQC | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
### Quantification Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Salmon Quantification
salmon\_quant
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Salmon Mapping and Quantification
salmon\_mapping\_quant
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### Read Mapping Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Bowtie2 FASTA Indexer
bowtie2\_fasta\_indexer
| Building reference for Bowite2 alignment (`bowtie2`: `bowtie2-build`) | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Bowtie2 FASTQ Read Mapper
bowtie2\_fastq\_read\_mapper
| Short read alignment (`bowtie2`, SAMtools view, SAMtools sort, SAMtools index) | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| BWA FASTA Indexer
bwa\_fasta\_indexer
| Building reference for BWA alignment (BWA- bwa index) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| BWA-MEM FASTQ Read Mapper
bwa\_mem\_fastq\_read\_mapper
| Short read alignment (BWA-MEM) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| STAR Generate Genome Index
star\_generate\_genome\_index
| RNA Seq- indexing ([STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) (`--runMode genomeGenerate`)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| STAR Mapping
star\_mapping
| RNA Seq- mapping ([STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Subread featureCounts
subread\_feature\_counts
| Read summarization, RNAseq (featureCounts) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Salmon Index Builder
salmon\_index\_builder
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Salmon Mapping and Quantification
salmon\_mapping\_quant
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### Read Manipulation Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)
gatk4\_bqsr\_parallel
| GATK4 - [BaseRecalibrator](https://gatk.broadinstitute.org/hc/en-us/articles/360046222991-BaseRecalibrator) and [ApplyBQSR](https://gatk.broadinstitute.org/hc/en-us/articles/360046222011-ApplyBQSR) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| Flexbar FASTQ Read Trimmer
flexbar\_fastq\_read\_trimmer
| [`flexbar`](https://github.com/seqan/flexbar/wiki) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Trimmomatic
trimmomatic
| Read quality trimming, adapter trimming ([`trimmomatic`](https://github.com/usadellab/Trimmomatic)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### RNAseq Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------- |
| RNASeQC
rnaseqc
| Transcriptomics Expression Quantification ([RNASeQC 2](https://github.com/getzlab/rnaseqc)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| STAR Generate Genome Index
star\_generate\_genome\_index
| RNA Seq- indexing ([STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) (`--runMode genomeGenerate`)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| STAR Mapping
star\_mapping
| RNA Seq- mapping ([STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Subread featureCounts
subread\_feature\_counts
| Read summarization, RNAseq (featureCounts) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| STAR Generate Genome Index
star\_generate\_genome\_index
| Transcriptomics Expression Quantification ([STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) (`--runMode genomeGenerate`)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| STAR Mapping
star\_mapping
| Transcriptomics Expression Quantification ([STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Salmon Index Builder
salmon\_index\_builder
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Salmon Mapping and Quantification
salmon\_mapping\_quant
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Salmon Quantification
salmon\_quant
| Transcriptomics Expression Quantification (Salmon) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### RNAseq Notebooks
Tutorial notebooks for transcriptomics expression analysis from the [`dnanexus/OpenBio`](https://github.com/dnanexus/OpenBio/tree/master/transcriptomics/tutorial_notebooks) repository:
* [Notebook 1: Expression Data Transformation](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-01_Transformation_R.ipynb) — Transform individual gene expression files into a gene counts matrix
* [Notebook 1B: Transformation from Dataset](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-01B_Transformation_from_Dataset.ipynb) — Transform dataset-backed expression data into an analysis-ready matrix
* [Notebook 2: Differential Expression Analysis](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb) — Differential expression analysis using DESeq2
* [Notebook 3: Gene Set Enrichment Analysis](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb) — Gene set enrichment analysis using WebGestaltR
* [Notebook 4: Gene Co-Expression Analysis](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb) — Co-expression network construction and analysis using WGCNA and topGO
* [Notebook 5: Gene Regulatory Network](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb) — Gene regulatory network inference using GENIE3
### Utility Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| File Concatenator
file\_concatenator
| File concatenation | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Gzip File Compressor
gzip
| gzip | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| Swiss Army Knife
swiss-army-knife
| Data processing tools (`bcftools`, `bedtools`, `bgzip`, `plink`, `sambamba`, `SAMtools`, `seqtk`, `tabix`, `vcflib`, `Plato`, `QCTool`, `vcftools`, `plink2`, `Picard`, `REGENIE`, `BOLT-LMM`, `BGEN`) | All regions |
| ttyd
ttyd
| Unix shell on a platform cloud worker in your browser. Use it for on-demand CLI operations and to launch httpsApp-enabled apps or applets on 2 extra ports | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
### Variant Calling Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| CNVkit
cnvkit\_batch
| Copy Number Variant ([CNVkit](https://cnvkit.readthedocs.io/en/stable/)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)
gatk4\_haplotypecaller\_parallel
| Variant calling, post-alignment QC ([GATK4- HaplotypeCaller module](https://gatk.broadinstitute.org/hc/en-us/articles/360045799892-HaplotypeCaller)) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)
gatk4\_genotypegvcfs\_single\_sample\_parallel
| [GATK4- GenotypeGVCFs module](https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
OCI: US (East)
|
| Picard MarkDuplicates Mappings Deduplicator
picard\_mark\_duplicates
| Variant Calling- remove duplicates, post-alignment ([MarkDuplicates from the Picard suite of tools](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| FreeBayes Variant Caller
freebayes
| Use for short variant calls ([FreeBayes](https://github.com/freebayes/freebayes/blob/master/README.md)) | AWS: US (East), Europe (Frankfurt), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| GATK4 Mutect2 Variant Caller and Filter
gatk4\_mutect2\_variant\_caller\_and\_filter
| Somatic variant calling and post calling filtering ([GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
| GATK4 Somatic Panel Of Normals Builder
gatk4\_somatic\_panel\_of\_normals\_builder
| Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2. ([GATK CreateSomaticPanelOfNormals](https://gatk.broadinstitute.org/hc/en-us/articles/5358921041947-CreateSomaticPanelOfNormals-BETA)) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain
Azure: US (West), Amsterdam
|
### Visualization Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------------- | ------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| LocusZoom
locuszoom
| GWAS, visualization (LocusZoom) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
### Nextflow Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| nf-core RNA-seq Pipeline
nfcore\_pipeline\_rnaseq
| Bulk RNA-seq processing from FASTQ or BAM ([`nf-core/rnaseq` v3.24.0](https://nf-co.re/rnaseq/3.24.0): QC, trimming, alignment with STAR or HiSAT2, and quantification with Salmon or RSEM) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
OCI: US (East)
|
| nf-core Sarek Pipeline
nfcore\_pipeline\_sarek
| Germline and somatic variant calling for WGS or targeted data ([`nf-core/sarek` v3.8.1](https://nf-co.re/sarek/3.8.1): germline and somatic variant calling with GATK HaplotypeCaller, Mutect2, DeepVariant, and Manta) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
OCI: US (East)
|
| nf-core scRNA-seq Pipeline
nfcore\_pipeline\_scrnaseq
| 10x Genomics single-cell RNA-seq processing and quantification ([`nf-core/scrnaseq` v4.1.0](https://nf-co.re/scrnaseq/4.1.0): 10x single-cell RNA-seq with STARsolo, SimpleAF or Alevin-Fry, Kallisto or BUStools, and CellRanger) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
OCI: US (East)
|
## Titan Tools
{% hint style="info" %}
A Titan license is required to access and use these tools. Contact [DNAnexus Sales](mailto:sales@dnanexus.com) for more information.
{% endhint %}
### Statistics Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| JupyterLab with ML
dxjupyterlab
Requires feature option ML (CLI: -ifeature=ML)
| Running analyses, visualizing data, building and testing models and algorithms in an interactive way (`dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `cntk`, `keras`, `scikit-learn`, `TensorFlow`, `torch`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam, OFH-TRE (London)
OCI: US (East)
|
| JupyterLab with Python\_R
dxjupyterlab
Requires feature option PYTHON\_R (CLI: -ifeature=PYTHON\_R, default)
| Running analyses, visualizing data, building and testing models and algorithms in an interactive way (`dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `BiocManager`, `coloc`, `epiR`, `incidence`, `MendelianRandomization`, `outbreaks`, `prevalence`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam, OFH-TRE (London)
OCI: US (East)
|
| JupyterLab with Stata
dxjupyterlab
Requires feature option STATA (CLI: -ifeature=STATA) and a Stata license
| Running analyses, visualizing data, building and testing models and algorithms in an interactive way, accessing and manipulating data in spark databases and tables (`dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `BiocManager`, `coloc`, `epiR`, `incidence`, `MendelianRandomization`, `outbreaks`, `prevalence`, `Stata`, `stata_kernel`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam, OFH-TRE (London)
OCI: US (East)
|
| JupyterLab with IMAGE\_PROCESSING
dxjupyterlab
Requires feature option IMAGE\_PROCESSING (CLI: -ifeature=IMAGE\_PROCESSING)
| Running imaging processing related analysis (`dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `nipype`, `freesurfer`, `FSL`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam, OFH-TRE (London)
OCI: US (East)
|
| JupyterLab with MONAI\_ML
dxjupyterlab
Requires feature option MONAI\_ML (CLI: -ifeature=MONAI\_ML)
| Running image processing related analysis, building and testing models and algorithms in an interactive way (`dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `keras`, `scikit-learn`, `TensorFlow`, `torch`, `monai`, `monailabel`, `3D Slicer`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam, OFH-TRE (London)
OCI: US (East)
|
## Apollo Tools
{% hint style="info" %}
An Apollo license is required to access and use these tools. Contact [DNAnexus Sales](mailto:sales@dnanexus.com) for more information.
{% endhint %}
### Dataset Administration Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ------------------------------------------------------------------------------------------------------------------------------------- | ------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------- |
| Data Model Loader
data\_model\_loader\_v2
| Dataset Creation | AWS: US (East), Europe (Frankfurt), Europe (London)
Azure: US (West), OFH-TRE (London)
|
| Dataset Extender
dataset-extender
| Dataset Extension | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London)
Azure: US (West), OFH-TRE (London)
|
### Dataset Management Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ------------------------------------------------------------------------------------------------------------------------- | --------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- |
| CSV Loader
csv-loader
| Data Loading | AWS: US (East), Europe (Frankfurt), Europe (London)
Azure: US (West)
|
| Spark SQL Runner
spark-sql-runner
| Dynamic SQL Execution (Spark SQL) | AWS: US (East), Europe (Frankfurt), Europe (London)
Azure: US (West), OFH-TRE (London)
|
| Table Exporter
table-exporter
| Data Extraction | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London)
Azure: US (West), OFH-TRE (London)
|
### Data Science Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- |
| JupyterLab with Spark Cluster with Glow
dxjupyterlab\_spark\_cluster
Requires feature option GLOW (CLI: -ifeature=GLOW)
| Running analyses, visualizing data, building and testing models and algorithms in an interactive way (`dxpy`, `hail`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `pyOpenSSL`, `glow.py`, `pypandoc`, `koalas`, `pyarrow`, `bokeh`, `vep`, `BiocManager`, `coloc`, `epiR`, `incidence`, `MendelianRandomization`, `outbreaks`, `prevalence`, `sparklyr`, `Glow`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London)
Azure: US (West), OFH-TRE (London)
|
| JupyterLab with Spark Cluster with Hail
dxjupyterlab\_spark\_cluster
Requires feature option HAIL (CLI: -ifeature=HAIL, default)
| Running analyses, visualizing data, building and testing models and algorithms in an interactive way (`dxpy`, `hail`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `pyOpenSSL`, `glow.py`, `pypandoc`, `koalas`, `pyarrow`, `bokeh`, `vep`, `BiocManager`, `coloc`, `epiR`, `incidence`, `MendelianRandomization`, `outbreaks`, `prevalence`, `sparklyr`, `HAIL`) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London)
Azure: US (West), OFH-TRE (London)
|
| JupyterLab with Spark Cluster with Hail and VEP
dxjupyterlab\_spark\_cluster
Requires feature option HAIL-VEP (CLI: -ifeature=HAIL-VEP)
| Running analyses, visualizing data, building and testing models and algorithms in an interactive way (`dxpy`, `hail`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `pyOpenSSL`, `glow.py`, `pypandoc`, `koalas`, `pyarrow`, `bokeh`, `vep`, `BiocManager`, `coloc`, `epiR`, `incidence`, `MendelianRandomization`, `outbreaks`, `prevalence`, `sparklyr`, `HAIL`, Ensembl Variant Effect Predictor) | AWS: US (East), Europe (Frankfurt), Europe (London), UKB-RAP (London)
Azure: US (West), OFH-TRE (London)
|
## Third Party Tools
Tools in the following categories are created and maintained by their respective vendors and may require separate licenses.
### DNAseq Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- |
| Sentieon somatic FASTQ to VCF
sentieon-tnseq
| WGS, WES, accelerated analysis (Sentieon's FASTQ to VCF somatic analysis pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Sentieon BWA-MEM and Sentieon De-duplication
sentieon-bwa
| WGS, WES, accelerated analysis (Sentieon's FASTQ to BAM/CRAM pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Germline Pipeline (NVIDIA Clara Parabricks accelerated)
pbgermline
| WGS, WES, accelerated analysis (BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration) | **AWS:** US (East), Europe (Frankfurt), Asia Pacific (Sydney) |
| Sentieon somatic BAM/CRAM to VCF
sentieon-tnbam
| WGS, WES, accelerated analysis (Sentieon's BAM to VCF somatic analysis pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| DeepVariant Pipeline (Parabricks accelerated)
pbdeepvariant
| Variant calling, accelerated analysis (Deepvariant) | **AWS:** US (East), Europe (Frankfurt), Asia Pacific (Sydney) |
| Sentieon UMI
sentieon-umi
| WGS, WES, accelerated analysis (Sentieon's pre-processing and alignment pipeline for next-generation sequence) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Sentieon germline BAM/CRAM to VCF
sentieon-dnabam
| WGS, WES, accelerated analysis (Sentieon's BAM to VCF germline analysis pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Sentieon distributed Joint Genotyping
sentieon-joint\_genotyping
| WGS, WES, accelerated analysis (Sentieon GVCFtyper) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Sentieon germline FASTQ to VCF
sentieon-dnaseq
| WGS, WES, accelerated analysis (Sentieon's FASTQ to VCF germline analysis pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
### Joint Cohort Genotyping Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- |
| Sentieon distributed Joint Genotyping
sentieon-joint\_genotyping
| WGS, WES, accelerated analysis (Sentieon GVCFtyper) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
### Read Mapping Apps
| Tool & CLI Command | Focus & Algorithms | Regions |
| ---------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- |
| Sentieon somatic FASTQ to VCF
sentieon-tnseq
| WGS, WES, accelerated analysis (Sentieon's FASTQ to VCF somatic analysis pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Sentieon BWA-MEM and Sentieon De-duplication
sentieon-bwa
| WGS, WES, accelerated analysis (Sentieon's FASTQ to BAM/CRAM pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Germline Pipeline (NVIDIA Clara Parabricks accelerated)
pbgermline
| WGS, WES, accelerated analysis (BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration) | **AWS:** US (East), Europe (Frankfurt), Asia Pacific (Sydney) |
| DeepVariant Pipeline (Parabricks accelerated)
pbdeepvariant
| Variant calling, accelerated analysis (Deepvariant) | **AWS:** US (East), Europe (Frankfurt), Asia Pacific (Sydney) |
| Sentieon UMI
sentieon-umi
| WGS, WES, accelerated analysis (Sentieon's pre-processing and alignment pipeline for next-generation sequence) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
| Sentieon germline FASTQ to VCF
sentieon-dnaseq
| WGS, WES, accelerated analysis (Sentieon's FASTQ to VCF germline analysis pipeline) | AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney)
Azure: US (West), Amsterdam
|
---
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