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Tools List

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

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
Retrieve reads in FASTQ format from SRA
​

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
oqfe
A revision of Functionally Equivalent​
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
​Strelka2 Germline Caller​
strelka2_germline
​Strelka2​
Small variant calling, Germline, WGS, WES
​Strelka2 Somatic Caller​
strelka2_somatic
​Strelka2​
Small variant calling, Somatic analysis

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
​PLINK GWAS​
plink_gwas
PLINK2
raremetal2
RAREMETALWORKER, RAREMETAL
saige_gwas_gbat
​SAIGE​
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

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

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
​SRA FASTQ Importer​
sra_fastq_importer
Retrieve reads in FASTQ format from SRA
​URL Fetcher​
url_fetcher
N/A
Fetches a file from a URL onto the DNAnexus platform

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

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

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
picard_samtools_fasta_indexer
CreateSequenceDictionary command from the Picard suite of tools, samtools faidx from Samtools.
Read Mapping
picard_collect_multiple_metrics
QC- statistic metrics for mapped reads
samtools_index
​SAMtools- samtools index
Building bam index file
​SAMtools Mappings Sorter​
samtools_sort
​SAMtools- samtools sort
Sort alignment result based on coordinates

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

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

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_rna_bam_eval
RSeQC
Transcriptomics Expression Quantification
fastqc
FastQC
jellyfish_and_genomescope
Jellyfish, GenomeScope
k-mer counting

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_quant
Salmon
Transcriptomics Expression Quantification

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, samtools view, samtools sort, samtools index
Short read alignment
​BWA FASTA Indexer​
bwa_fasta_indexer
BWA- bwa index
Building reference for BWA alignment
minimap2_align_longread
minimap2, biobambam2
Read Mapping of PacBio and ONT long reads
bwa_mem_fastq_read_mapper
BWA-MEM
Short read alignment
​HISAT2 Index​
hisat2_index
Transcriptomics
​HISAT2 Mapper​
hisat2_mapper
Transcriptomics
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 (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_quant
Salmon
Transcriptomics Expression Quantification

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
gatk4_bqsr_parallel
Variant calling
flexbar_fastq_read_trimmer
​Flexbar​
QC
​Trimmomatic​
trimmomatic
​trimmomatic​
Read quality trimming, adapter trimming

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
​RNASeQC​
rnaseqc
​RNAseqC 2​
Transcriptomics Expression Quantification
rseqc_rna_bam_eval
RSeQC
Transcriptomics Expression Quantification
​HISAT2 Index​
hisat2_index
Transcriptomics
​HISAT2 Mapper​
hisat2_mapper
Transcriptomics
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 (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_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

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
​

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

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
​Copy File​
dxwdl_copy_file
N/A
​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

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
​CNVkit​
cnvkit_batch
​CNVkit​
Copy Number Variant
deepvariant_germline
​DeepVariant​
Variant calling
​Parliament2​
parliament2
Breakdancer, BreakSeq2, CNVnator, Delly, Lumpy, Manta, SVTyper, svviz, SURVIVOR
Structural variants
gatk4_haplotypecaller_parallel
Variant calling, post-alignment QC
gatk4_genotypegvcfs_single_sample_parallel
Variant calling
picard_mark_duplicates
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
​GATK Mutect2​
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.

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
​LocusZoom​
locuszoom
LocusZoom
GWAS, visualization

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

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
dxjupyterlab
dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn , dxdata, nipype, freesurfer, FSL
Running imaging processing related analysis

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

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

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

​
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

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

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-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

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
sentieon-joint_genotyping
Sentieon GVCFtyper
WGS, WES, accelerated analysis

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-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

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
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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
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Utility Apps
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Dataset Management Apps
Data Science Apps
Third Party Tools
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Read Mapping Apps
Variant Calling Apps