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)	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)	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 and 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)	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	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)	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)	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)	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)	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)	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)	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)	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, MONAI Label)	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)	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 - 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 - 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)	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 (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 (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 and 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	AWS: US (East), Europe (Frankfurt), Europe (London), Asia Pacific (Sydney), Bahrain Azure: US (West), Amsterdam
Trimmomatic trimmomatic	Read quality trimming, adapter trimming (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)	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 (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 (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 (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 (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 repository:

• Notebook 1: Expression Data Transformation — Transform individual gene expression files into a gene counts matrix

• Notebook 1B: Transformation from Dataset — Transform dataset-backed expression data into an analysis-ready matrix

• Notebook 2: Differential Expression Analysis — Differential expression analysis using DESeq2

• Notebook 3: Gene Set Enrichment Analysis — Gene set enrichment analysis using WebGestaltR

• Notebook 4: Gene Co-Expression Analysis — Co-expression network construction and analysis using WGCNA and topGO

• Notebook 5: Gene Regulatory Network — 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)	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)	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	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)	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)	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)	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)	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: 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: 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: 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

A Titan license is required to access and use these tools. Contact DNAnexus Sales for more information.

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

An Apollo license is required to access and use these tools. Contact DNAnexus Sales for more information.

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