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_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
	star_generate_genome_index		Transcriptomics Expression Quantification
	star_mapping		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_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

Visualization Apps

Name of Tool	Name in CLI	Scientific Algorithms	Common Uses
	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
	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

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_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