DNAnexus Documentation
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Copyright 2025 DNAnexus

On this page
  • Public Tools
  • Annotation Apps
  • Data Transfer Apps
  • DNAseq Apps
  • GWAS Apps
  • File Transfer Apps
  • Import Apps
  • Interactive Analysis Apps
  • Joint Genotyping Apps
  • Mapping Manipulation Apps
  • PheWAS Apps
  • PRS Apps
  • QC Apps
  • Quantification Apps
  • Read Mapping Apps
  • Read Manipulation Apps
  • RNAseq Apps
  • RNAseq Notebooks
  • Utility Apps
  • Variant Calling Apps
  • Visualization Apps
  • Titan Tools
  • Statistics Apps
  • Apollo Tools
  • Dataset Administration Apps
  • Dataset Management Apps
  • Data Science Apps
  • Third Party Tools
  • DNAseq Apps
  • Joint Cohort Genotyping Apps
  • Read Mapping Apps
  • Variant Calling Apps

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  1. User
  2. Running Apps and Workflows

Tools List

Public Tools

Annotation Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

snpeff_annotate

SnpEff

Annotation

snpsift_annotate

SnpSift

Annotation

Data Transfer Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common uses

aws_platform_to_s3_file_transfer

AWS S3

aws_s3_to_platform_files

AWS S3

sra_fastq_importer

Retrieve reads in FASTQ format from SRA

DNAseq Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

oqfe

WGS, WES- alignment and duplicate marking

gatk4_bqsr_parallel

Variant calling

bwa_mem_fastq_read_mapper

BWA-MEM

Short read alignment

gatk4_haplotypecaller_parallel

Variant calling, post-alignment QC

gatk4_genotypegvcfs_single_sample_parallel

Variant calling

picard_mark_duplicates

Variant Calling- remove duplicates, post-alignment

GWAS Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

regenie

REGENIE

GWAS

plink_gwas

PLINK2

raremetal2

RAREMETALWORKER, RAREMETAL

saige_gwas_gbat

saige_gwas_svat

saige_gwas_grm

saige_gwas_sparse_grm

plink_pipeline

Plink2

plato_pipeline

Plato, Plink2

locuszoom

LocusZoom

GWAS, visualization

File Transfer Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

url_fetcher

N/A

Fetches a file from a URL onto the DNAnexus platform

Import Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

sra_fastq_importer

Retrieve reads in FASTQ format from SRA

url_fetcher

N/A

Fetches a file from a URL onto the DNAnexus platform

Interactive Analysis Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

cloud_workstation

N/A

SSH-accessible unix shell on a platform cloud worker. Use it for ad hoc analysis of platform data.

ttyd

N/A

Unix shell on a platform cloud worker in your browser. Use it for ad hoc CLI operations and to launch https apps on 2 extra ports

Joint Genotyping Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

glnexus

GLnexus

This app can also be used to create pVCF without running joint genotyping

Mapping Manipulation Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

samtools_index

Building bam index file

samtools_sort

Sort alignment result based on coordinates

PheWAS Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

phesant

PHESANT

PheWAS

PRS Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

prsice2

PRSice-2

Polygenic risk scores

QC Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

multiqc

MultiQC

QC reporting

qualimap2_anlys

Qualimap2

QC

rnaseqc

Transcriptomics Expression Quantification

fastqc

FastQC

Quantification Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

salmon_quant

Salmon

Transcriptomics Expression Quantification

salmon_mapping_quant

Salmon

Transcriptomics Expression Quantification

Read Mapping Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

bowtie2_fasta_indexer

Bowtie 2: bowtie2-build

Building reference for Bowite2 alignment

bowtie2_fastq_read_mapper

bowtie2, samtools view, samtools sort, samtools index

Short read alignment

bwa_fasta_indexer

BWA- bwa index

Building reference for BWA alignment

bwa_mem_fastq_read_mapper

BWA-MEM

Short read alignment

star_generate_genome_index

RNA Seq- indexing

star_mapping

RNA Seq- mapping

subread_feature_counts

featureCounts

Read summarization, RNAseq

salmon_index_builder

Salmon

Transcriptomics Expression Quantification

salmon_mapping_quant

Salmon

Transcriptomics Expression Quantification

Read Manipulation Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

gatk4_bqsr_parallel

Variant calling

flexbar_fastq_read_trimmer

QC

trimmomatic

Read quality trimming, adapter trimming

RNAseq Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

rnaseqc

Transcriptomics Expression Quantification

star_generate_genome_index

RNA Seq- indexing

star_mapping

RNA Seq- mapping

subread_feature_counts

featureCounts

Read summarization, RNAseq

star_generate_genome_index

Transcriptomics Expression Quantification

star_mapping

Transcriptomics Expression Quantification

salmon_index_builder

Salmon

Transcriptomics Expression Quantification

salmon_mapping_quant

Salmon

Transcriptomics Expression Quantification

salmon_quant

Salmon

Transcriptomics Expression Quantification

RNAseq Notebooks

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb

DESeq2

Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb

WebGestaltR

Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb

WGCNA, topGO

Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb

GENIE3

Utility Apps

Name of Tool

Name in CLI

Scientific Algorithm

Common Uses

file_concatenator

N/A

gzip

gzip

swiss-army-knife

bcftools, bedtools, bgzip, plink, sambamba, samtools, seqtk, tabix, vcflib, Plato, QCTool, vcftools, plink2, Picard, REGENIE, BOLT-LMM, BGEN

Data processing tools

ttyd

N/A

Unix shell on a platform cloud worker in your browser. Use it for ad hoc CLI operations and to launch https apps on 2 extra ports

Variant Calling Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

cnvkit_batch

Copy Number Variant

gatk4_haplotypecaller_parallel

Variant calling, post-alignment QC

gatk4_genotypegvcfs_single_sample_parallel

Variant calling

picard_mark_duplicates

Variant Calling- remove duplicates, post-alignment

freebayes

Use for short variant calls

gatk4_mutect2_variant_caller_and_filter

Somatic variant calling and post calling filtering

gatk4_somatic_panel_of_normals_builder

Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.

Visualization Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

locuszoom

LocusZoom

GWAS, visualization

Titan Tools

Statistics Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

dxjupyterlab

dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn , dxdata, cntk, keras,scikit-learn, tensorflow, torch

Running analyses, visualizing data, building and testing models and algorithms in an interactive way

dxjupyterlab

dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, BiocManager, coloc, epiR, hyprcoloc, incidence, MendelianRandomization, outbreaks, prevalence

Running analyses, visualizing data, building and testing models and algorithms in an interactive way

dxjupyterlab

dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, BiocManager, coloc, epiR, hyprcoloc, incidence, MendelianRandomization, outbreaks, prevalence, Stata, stata_kernel

Running analyses, visualizing data, building and testing models and algorithms in an interactive way, accessing and manipulating data in spark databases and tables

dxjupyterlab

dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn , dxdata, nipype, freesurfer, FSL

Running imaging processing related analysis

Apollo Tools

Dataset Administration Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

data_model_loader_v2

Dataset Creation

Dataset Creation

dataset-extender

Dataset Extension

Dataset Extension

Dataset Management Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

csv-loader

N/A

Data Loading

spark-sql-runner

Spark SQL

Dynamic SQL Execution

table-exporter

N/A

Data Extraction

Data Science Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

dxjupyterlab_spark_cluster

dxpy, hail, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, pyOpenSSL, glow.py, pypandoc, koalas, pyarrow, bokeh, vep, BiocManager, coloc, epiR, yprcoloc, incidence, MendelianRandomization, outbreaks, prevalence, sparklyr, Glow

Running analyses, visualizing data, building and testing models and algorithms in an interactive way

dxjupyterlab_spark_cluster

dxpy, hail, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, pyOpenSSL, glow.py, pypandoc, koalas, pyarrow, bokeh, vep, BiocManager, coloc, epiR, yprcoloc, incidence, MendelianRandomization, outbreaks, prevalence, sparklyr, HAIL

Running analyses, visualizing data, building and testing models and algorithms in an interactive way

dxjupyterlab_spark_cluster

dxpy, hail, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, pyOpenSSL, glow.py, pypandoc, koalas, pyarrow, bokeh, vep, BiocManager, coloc, epiR, yprcoloc, incidence, MendelianRandomization, outbreaks, prevalence, sparklyr, HAIL, Ensembl Variant Effect Predictor

Running analyses, visualizing data, building and testing models and algorithms in an interactive way

Third Party Tools

Tools in this section are created and maintained by their respective vendors and may require separate licenses.

DNAseq Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

sentieon-tnseq

Sentieon's FASTQ to VCF somatic analysis pipeline

WGS, WES, accelerated analysis

sentieon-bwa

Sentieon's FASTQ to BAM/CRAM pipeline

WGS, WES, accelerated analysis

pbgermline

BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration

WGS, WES, accelerated analysis

sentieon-tnbam

Sentieon's BAM to VCF somatic analysis pipeline

WGS, WES, accelerated analysis

pbdeepvariant

Deepvariant

Variant calling, accelerated analysis

sentieon-umi

Sentieon's pre-processing and alignment pipeline for next-generation sequence

WGS, WES, accelerated analysis

sentieon-dnabam

Sentieon's BAM to VCF germline analysis pipeline

WGS, WES, accelerated analysis

sentieon-joint_genotyping

Sentieon GVCFtyper

WGS, WES, accelerated analysis

sentieon-ccdg

Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline

WGS, WES, accelerated analysis

sentieon-dnaseq

Sentieon's FASTQ to VCF germline analysis pipeline

WGS, WES, accelerated analysis

Joint Cohort Genotyping Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

sentieon-joint_genotyping

Sentieon GVCFtyper

WGS, WES, accelerated analysis

Read Mapping Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

sentieon-tnseq

Sentieon's FASTQ to VCF somatic analysis pipeline

WGS, WES, accelerated analysis

sentieon-bwa

Sentieon's FASTQ to BAM/CRAM pipeline

WGS, WES, accelerated analysis

pbgermline

BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration

WGS, WES, accelerated analysis

pbdeepvariant

Deepvariant

Variant calling, accelerated analysis

sentieon-umi

Sentieon's pre-processing and alignment pipeline for next-generation sequence

WGS, WES, accelerated analysis

sentieon-ccdg

Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline

WGS, WES, accelerated analysis

sentieon-dnaseq

Sentieon's FASTQ to VCF germline analysis pipeline

WGS, WES, accelerated analysis

Variant Calling Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

sentieon-tnseq

Sentieon's FASTQ to VCF somatic analysis pipeline

WGS, WES, accelerated analysis, somatic variant calling

pbgermline

BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration

WGS, WES, accelerated analysis

sentieon-tnbam

Sentieon's BAM to VCF somatic analysis pipeline

WGS, WES, accelerated analysis, somatic variant calling

sentieon-dnabam

Sentieon's BAM to VCF germline analysis pipeline

WGS, WES, accelerated analysis

sentieon-joint_genotyping

Sentieon GVCFtyper

WGS, WES, accelerated analysis

sentieon-ccdg

Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline

WGS, WES, accelerated analysis

sentieon-dnaseq

Sentieon's FASTQ to VCF germline analysis pipeline

WGS, WES, accelerated analysis

pbmutectcaller

GPU accelerated version of Mutect2 and supports both tumor-only and tumor-normal variant calling

Last updated 3 months ago

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A revision of

- samtools index

- samtools sort

(Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)

(Spliced Transcripts Alignment to a Reference)

(Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)

(Spliced Transcripts Alignment to a Reference)

(Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)

(Spliced Transcripts Alignment to a Reference)

A Titan license is required to access and use these tools. Please contact for more information.

An Apollo license is required to access and use these tools. Please contact for more information.

DNAnexus Sales
DNAnexus Sales
SnpEff Annotate
SnpSift Annotate
AWS S3 Exporter
AWS S3 Importer
SRA FASTQ Importer
SRA toolkit's fasterq-dump
Original Quality Functionally Equivalent
Functionally Equivalent
GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)
GATK4- BaseRecalibrator and ApplyBQSR
BWA-MEM FASTQ Read Mapper
GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)
GATK4- HaplotypeCaller module
GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)
GATK4- GenotypeGVCFs module
Picard MarkDuplicates Mappings Deduplicator
MarkDuplicates from the Picard suite of tools
Regenie
PLINK GWAS
Raremetal2 - Raremetal and Raremetalworker
SAIGE GWAS - Gene and region based association tests
SAIGE
SAIGE GWAS - Single variant association tests
SAIGE
SAIGE GWAS GRM
SAIGE
SAIGE-GWAS Sparse GRM
SAIGE
Plink GWAS Pipeline
Plato GWAS Pipeline
LocusZoom
URL Fetcher
SRA FASTQ Importer
SRA toolkit's fasterq-dump
URL Fetcher
Cloud Workstation
ttyd
GLnexus
SAMtools Mappings Indexer
SAMtools
SAMtools Mappings Sorter
SAMtools
PHESANT
PRSice 2
MultiQC
Qualimap2 Analysis
RNASeQC
RNAseqC 2
FastQC Reads Quality Control
Salmon Quantification
Salmon Mapping and Quantification
Bowtie2 FASTA Indexer
Bowtie2 FASTQ Read Mapper
BWA FASTA Indexer
BWA-MEM FASTQ Read Mapper
STAR Generate Genome Index
STAR
STAR Mapping
STAR
Subread featureCounts
Salmon Index Builder
Salmon Mapping and Quantification
GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)
GATK4- BaseRecalibrator and ApplyBQSR
Flexbar FASTQ Read Trimmer
Flexbar
Trimmomatic
trimmomatic
RNASeQC
RNAseqC 2
STAR Generate Genome Index
STAR
STAR Mapping
STAR
Subread featureCounts
STAR Generate Genome Index
STAR
STAR Mapping
STAR
Salmon Index Builder
Salmon Mapping and Quantification
Salmon Quantification
Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb
Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb
Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb
Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb
File Concatenator
Gzip File Compressor
Swiss Army Knife
ttyd
CNVkit
CNVkit
GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)
GATK4- HaplotypeCaller module
GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)
GATK4- GenotypeGVCFs module
Picard MarkDuplicates Mappings Deduplicator
MarkDuplicates from the Picard suite of tools
FreeBayes Variant Caller
FreeBayes
GATK4 Mutect2 Variant Caller and Filter
GATK Mutect2
GATK4 Somatic Panel Of Normals Builder
GATK CreateSomaticPanelOfNormals
LocusZoom
JupyterLab with ML
JupyterLab with Python_R
JupyterLab with Stata
JupyterLab with IMAGE_PROCESSING
Data Model Loader
Dataset Extender
CSV Loader
Spark SQL Runner
Table exporter
JupyterLab with Spark Cluster with Glow
JupyterLab with Spark Cluster with Hail
JupyterLab with Spark Cluster with Hail and VEP
Sentieon somatic FASTQ to VCF
Sentieon BWA-MEM and Sentieon De-duplication
Germline Pipeline (Nvidia Clara Parabricks accelerated)
Sentieon somatic BAM/CRAM to VCF
DeepVariant Pipeline (Parabricks accelerated)
Sentieon UMI
Sentieon germline BAM/CRAM to VCF
Sentieon distributed Joint Genotyping
Sentieon Functional equivalent protocol
Sentieon germline FASTQ to VCF
Sentieon distributed Joint Genotyping
Sentieon somatic FASTQ to VCF
Sentieon BWA-MEM and Sentieon De-duplication
Germline Pipeline (Nvidia Clara Parabricks accelerated)
DeepVariant Pipeline (Parabricks accelerated)
Sentieon UMI
Sentieon Functional equivalent protocol
Sentieon germline FASTQ to VCF
Sentieon somatic FASTQ to VCF
Germline Pipeline (Nvidia Clara Parabricks accelerated)
Sentieon somatic BAM/CRAM to VCF
Sentieon germline BAM/CRAM to VCF
Sentieon distributed Joint Genotyping
Sentieon Functional equivalent protocol
Sentieon germline FASTQ to VCF
Mutectcaller (Parabricks accelerated)
NVIDIA's Clara Parabricks mutectcaller