Tools List

Public Tools

Annotation Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
SnpEff Annotate	snpeff_annotate	SnpEff	Annotation
SnpSift Annotate	snpsift_annotate	SnpSift	Annotation

Data Transfer Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common uses
AWS S3 Exporter	aws_platform_to_s3_file_transfer	AWS S3
AWS S3 Importer	aws_s3_to_platform_files	AWS S3
SRA FASTQ Importer	sra_fastq_importer	SRA toolkit's fasterq-dump	Retrieve reads in FASTQ format from SRA

DNAseq Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
Original Quality Functionally Equivalent	oqfe	A revision of Functionally Equivalent	WGS, WES- alignment and duplicate marking
GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)	gatk4_bqsr_parallel	GATK4- BaseRecalibrator and ApplyBQSR	Variant calling
BWA-MEM FASTQ Read Mapper	bwa_mem_fastq_read_mapper	BWA-MEM	Short read alignment
GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)	gatk4_haplotypecaller_parallel	GATK4- HaplotypeCaller module	Variant calling, post-alignment QC
GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)	gatk4_genotypegvcfs_single_sample_parallel	GATK4- GenotypeGVCFs module	Variant calling
Picard MarkDuplicates Mappings Deduplicator	picard_mark_duplicates	MarkDuplicates from the Picard suite of tools	Variant Calling- remove duplicates, post-alignment
Strelka2 Germline Caller	strelka2_germline	Strelka2	Small variant calling, Germline, WGS, WES
Strelka2 Somatic Caller	strelka2_somatic	Strelka2	Small variant calling, Somatic analysis

GWAS Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
Regenie	regenie	REGENIE	GWAS
PLINK GWAS	plink_gwas	PLINK2
Raremetal2 - Raremetal and Raremetalworker	raremetal2	RAREMETALWORKER, RAREMETAL
SAIGE GWAS - Gene and region based association tests	saige_gwas_gbat	SAIGE
SAIGE GWAS - Single variant association tests	saige_gwas_svat	SAIGE
SAIGE GWAS GRM	saige_gwas_grm	SAIGE
SAIGE-GWAS Sparse GRM	saige_gwas_sparse_grm	SAIGE
Plink GWAS Pipeline	plink_pipeline	Plink2
Plato GWAS Pipeline	plato_pipeline	Plato, Plink2
LocusZoom	locuszoom	LocusZoom	GWAS, visualization

File Transfer Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
URL Fetcher	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	sra_fastq_importer	SRA toolkit's fasterq-dump	Retrieve reads in FASTQ format from SRA
URL Fetcher	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	cloud_workstation	N/A	SSH-accessible unix shell on a platform cloud worker. Use it for ad hoc analysis of platform data.
ttyd	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	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
FASTA indexer (with Picard and Samtools)	picard_samtools_fasta_indexer	CreateSequenceDictionary command from the Picard suite of tools, samtools faidx from Samtools.	Read Mapping
Picard CollectMultipleMetrics	picard_collect_multiple_metrics	CollectMultipleMetrics command from the Picard suite of tools	QC- statistic metrics for mapped reads
SAMtools Mappings Indexer	samtools_index	SAMtools- samtools index	Building bam index file
SAMtools Mappings Sorter	samtools_sort	SAMtools- samtools sort	Sort alignment result based on coordinates

PheWAS Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
PHESANT	phesant	PHESANT	PheWAS

PRS Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
PRSice 2	prsice2	PRSice-2	Polygenic risk scores

QC Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
MultiQC	multiqc	MultiQC	QC reporting
Qualimap2 Analysis	qualimap2_anlys	Qualimap2	QC
RNASeQC	rnaseqc	RNAseqC 2	Transcriptomics Expression Quantification
RSeQC RNAseq Quality Control	rseqc_rna_bam_eval	RSeQC	Transcriptomics Expression Quantification
FastQC Reads Quality Control	fastqc	FastQC
Jellyfish and GenomeScope	jellyfish_and_genomescope	Jellyfish, GenomeScope	k-mer counting

Quantification Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
RSEM Calculate Express	rsem	RSEM	Transcriptomics Expression Quantification
Kallisto Quantification	kallisto	Kallisto	Transcriptomics Expression Quantification
Salmon Quantification	salmon_quant	Salmon	Transcriptomics Expression Quantification
Salmon Mapping and Quantification	salmon_mapping_quant	Salmon	Transcriptomics Expression Quantification

Read Mapping Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
Bowtie2 FASTA Indexer	bowtie2_fasta_indexer	Bowtie 2: bowtie2-build	Building reference for Bowite2 alignment
Bowtie2 FASTQ Read Mapper	bowtie2_fastq_read_mapper	bowtie2, samtools view, samtools sort, samtools index	Short read alignment
BWA FASTA Indexer	bwa_fasta_indexer	BWA- bwa index	Building reference for BWA alignment
Minimap2 Aligner for Long Reads	minimap2_align_longread	minimap2, biobambam2	Read Mapping of PacBio and ONT long reads
BWA-MEM FASTQ Read Mapper	bwa_mem_fastq_read_mapper	BWA-MEM	Short read alignment
HISAT2 Index	hisat2_index	HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts)	Transcriptomics
HISAT2 Mapper	hisat2_mapper	HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts)	Transcriptomics
STAR Generate Genome Index	star_generate_genome_index	STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)	RNA Seq- indexing
STAR Mapping	star_mapping	STAR (Spliced Transcripts Alignment to a Reference)	RNA Seq- mapping
Subread featureCounts	subread_feature_counts	featureCounts	Read summarization, RNAseq
STAR Generate Genome Index	star_generate_genome_index	STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)	Transcriptomics Expression Quantification
STAR Mapping	star_mapping	STAR (Spliced Transcripts Alignment to a Reference)	Transcriptomics Expression Quantification
Salmon Index Builder	salmon_index_builder	Salmon	Transcriptomics Expression Quantification
Salmon Mapping and Quantification	salmon_mapping_quant	Salmon	Transcriptomics Expression Quantification

Read Manipulation Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)	gatk4_bqsr_parallel	GATK4- BaseRecalibrator and ApplyBQSR	Variant calling
Flexbar FASTQ Read Trimmer	flexbar_fastq_read_trimmer	Flexbar	QC
Trimmomatic	trimmomatic	trimmomatic	Read quality trimming, adapter trimming

RNAseq Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
STAR Fusion Caller	star_fusion_caller	STAR-Fusion	RNA-Seq fusion calling
GATK Haplotypecaller and Filter for RNAseq	gatk4_haplotypecaller_rnaseq	GATK best practice workflow for RNAseq short variant discovery (SNPs + Indels)(SplitNCigarReads, HaplotypeCaller, VariantFiltration)	RNA-seq variant calling, post-alignment QC
RNASeQC	rnaseqc	RNAseqC 2	Transcriptomics Expression Quantification
RSeQC RNAseq Quality Control	rseqc_rna_bam_eval	RSeQC	Transcriptomics Expression Quantification
HISAT2 Index	hisat2_index	HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts)	Transcriptomics
HISAT2 Mapper	hisat2_mapper	HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts)	Transcriptomics
STAR Generate Genome Index	star_generate_genome_index	STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)	RNA Seq- indexing
STAR Mapping	star_mapping	STAR (Spliced Transcripts Alignment to a Reference)	RNA Seq- mapping
Subread featureCounts	subread_feature_counts	featureCounts	Read summarization, RNAseq
STAR Generate Genome Index	star_generate_genome_index	STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)	Transcriptomics Expression Quantification
STAR Mapping	star_mapping	STAR (Spliced Transcripts Alignment to a Reference)	Transcriptomics Expression Quantification
Salmon Index Builder	salmon_index_builder	Salmon	Transcriptomics Expression Quantification
Salmon Mapping and Quantification	salmon_mapping_quant	Salmon	Transcriptomics Expression Quantification
Kallisto Index Builder	kallisto_index_builder	Kallisto	Transcriptomics Expression Quantification
RSEM Calculate Express	rsem	RSEM	Transcriptomics Expression Quantification
Kallisto Quantification	kallisto	Kallisto	Transcriptomics Expression Quantification
Salmon 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	Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb	DESeq2
Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb	Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb	WebGestaltR
Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb	Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb	WGCNA, topGO
Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb	Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb	GENIE3

RNAseq Global Workflows

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
TEQ - Transcriptomic Expression Quantification	transcriptomic_expression_quantification	FastQC, Trimmomatic, STAR, RSEM, Kallisto, Salmon, RNA-SeQC2, RSeQC, MultiQC

Utility Apps

Name of Tool	Name in CLI	Scientific Algorithm	Common Uses
File Concatenator	file_concatenator	N/A
Gzip File Compressor	gzip	gzip
Swiss Army Knife	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	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
STAR Fusion Caller	star_fusion_caller	STAR-Fusion	RNA-Seq fusion calling
GATK Haplotypecaller and Filter for RNAseq	gatk4_haplotypecaller_rnaseq	GATK best practice workflow for RNAseq short variant discovery (SNPs + Indels)(SplitNCigarReads, HaplotypeCaller, VariantFiltration)	RNA-seq variant calling, post-alignment QC
CNVkit	cnvkit_batch	CNVkit	Copy Number Variant
DeepVariant Germline Variant Caller	deepvariant_germline	DeepVariant	Variant calling
Parliament2	parliament2	Breakdancer, BreakSeq2, CNVnator, Delly, Lumpy, Manta, SVTyper, svviz, SURVIVOR	Structural variants
GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)	gatk4_haplotypecaller_parallel	GATK4- HaplotypeCaller module	Variant calling, post-alignment QC
GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)	gatk4_genotypegvcfs_single_sample_parallel	GATK4- GenotypeGVCFs module	Variant calling
Picard MarkDuplicates Mappings Deduplicator	picard_mark_duplicates	MarkDuplicates from the Picard suite of tools	Variant Calling- remove duplicates, post-alignment
Strelka2 Germline Caller	strelka2_germline	Strelka2	Small variant calling, Germline, WGS, WES
Strelka2 Somatic Caller	strelka2_somatic	Strelka2	Small variant calling, Somatic analysis
FreeBayes Variant Caller	freebayes	FreeBayes	Use for short variant calls
GATK4 Mutect2 Variant Caller and Filter	gatk4_mutect2_variant_caller_and_filter	GATK Mutect2	Somatic variant calling and post calling filtering
GATK4 Somatic Panel Of Normals Builder	gatk4_somatic_panel_of_normals_builder	GATK CreateSomaticPanelOfNormals	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	LocusZoom	GWAS, visualization

Titan Tools

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

Statistics Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
JupyterLab with ML	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
JupyterLab with Python_R	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
JupyterLab with Stata	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
JupyterLab with IMAGE_PROCESSING	dxjupyterlab	dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn , dxdata, nipype, freesurfer, FSL	Running imaging processing related analysis

Apollo Tools

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

Dataset Administration Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
Data Model Loader	data_model_loader_v2	Dataset Creation	Dataset Creation
Dataset Extender	dataset-extender	Dataset Extension	Dataset Extension

Dataset Management Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
CSV Loader	csv-loader	N/A	Data Loading
Spark SQL Runner	spark-sql-runner	Spark SQL	Dynamic SQL Execution
Table exporter	table-exporter	N/A	Data Extraction

Data Science Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
JupyterLab with Spark Cluster with Glow	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
JupyterLab with Spark Cluster with Hail	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
JupyterLab with Spark Cluster with Hail and VEP	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 somatic FASTQ to VCF	sentieon-tnseq	Sentieon's FASTQ to VCF somatic analysis pipeline	WGS, WES, accelerated analysis
Sentieon BWA-MEM and Sentieon De-duplication	sentieon-bwa	Sentieon's FASTQ to BAM/CRAM pipeline	WGS, WES, accelerated analysis
Germline Pipeline (Nvidia Clara Parabricks accelerated)	pbgermline	BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration	WGS, WES, accelerated analysis
Sentieon somatic BAM/CRAM to VCF	sentieon-tnbam	Sentieon's BAM to VCF somatic analysis pipeline	WGS, WES, accelerated analysis
DeepVariant Pipeline (Parabricks accelerated)	pbdeepvariant	Deepvariant	Variant calling, accelerated analysis
Sentieon UMI	sentieon-umi	Sentieon's pre-processing and alignment pipeline for next-generation sequence	WGS, WES, accelerated analysis
Sentieon germline BAM/CRAM to VCF	sentieon-dnabam	Sentieon's BAM to VCF germline analysis pipeline	WGS, WES, accelerated analysis
Sentieon distributed Joint Genotyping	sentieon-joint_genotyping	Sentieon GVCFtyper	WGS, WES, accelerated analysis
Sentieon Functional equivalent protocol	sentieon-ccdg	Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline	WGS, WES, accelerated analysis
Sentieon germline FASTQ to VCF	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 distributed Joint Genotyping	sentieon-joint_genotyping	Sentieon GVCFtyper	WGS, WES, accelerated analysis

Read Mapping Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
Sentieon somatic FASTQ to VCF	sentieon-tnseq	Sentieon's FASTQ to VCF somatic analysis pipeline	WGS, WES, accelerated analysis
Sentieon BWA-MEM and Sentieon De-duplication	sentieon-bwa	Sentieon's FASTQ to BAM/CRAM pipeline	WGS, WES, accelerated analysis
Germline Pipeline (Nvidia Clara Parabricks accelerated)	pbgermline	BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration	WGS, WES, accelerated analysis
DeepVariant Pipeline (Parabricks accelerated)	pbdeepvariant	Deepvariant	Variant calling, accelerated analysis
Sentieon UMI	sentieon-umi	Sentieon's pre-processing and alignment pipeline for next-generation sequence	WGS, WES, accelerated analysis
Sentieon Functional equivalent protocol	sentieon-ccdg	Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline	WGS, WES, accelerated analysis
Sentieon germline FASTQ to VCF	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 somatic FASTQ to VCF	sentieon-tnseq	Sentieon's FASTQ to VCF somatic analysis pipeline	WGS, WES, accelerated analysis, somatic variant calling
Germline Pipeline (Nvidia Clara Parabricks accelerated)	pbgermline	BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration	WGS, WES, accelerated analysis
Sentieon somatic BAM/CRAM to VCF	sentieon-tnbam	Sentieon's BAM to VCF somatic analysis pipeline	WGS, WES, accelerated analysis, somatic variant calling
Sentieon germline BAM/CRAM to VCF	sentieon-dnabam	Sentieon's BAM to VCF germline analysis pipeline	WGS, WES, accelerated analysis
Sentieon distributed Joint Genotyping	sentieon-joint_genotyping	Sentieon GVCFtyper	WGS, WES, accelerated analysis
Sentieon Functional equivalent protocol	sentieon-ccdg	Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline	WGS, WES, accelerated analysis
Sentieon germline FASTQ to VCF	sentieon-dnaseq	Sentieon's FASTQ to VCF germline analysis pipeline	WGS, WES, accelerated analysis
Mutectcaller (Parabricks accelerated)	pbmutectcaller	NVIDIA's Clara Parabricks mutectcaller	GPU accelerated version of Mutect2 and supports both tumor-only and tumor-normal variant calling