Tools List
Public Tools
Annotation Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
Data Transfer Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common uses
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
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
Small variant calling, Germline, WGS, WES
GWAS Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
File Transfer Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
Import Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
sra_fastq_importer
Retrieve reads in FASTQ format from SRA
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
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_sort
Sort alignment result based on coordinates
PheWAS Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
PRS Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
QC Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
Quantification Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
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
minimap2_align_longread
minimap2, biobambam2
Read Mapping of PacBio and ONT long reads
hisat2_index
Transcriptomics
hisat2_mapper
Transcriptomics
star_generate_genome_index
RNA Seq- indexing
star_mapping
RNA Seq- mapping
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
RNAseq Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
hisat2_index
Transcriptomics
hisat2_mapper
Transcriptomics
star_generate_genome_index
RNA Seq- indexing
star_mapping
RNA Seq- mapping
star_generate_genome_index
Transcriptomics Expression Quantification
star_mapping
Transcriptomics Expression Quantification
salmon_mapping_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
​
RNAseq Global Workflows
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
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
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
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
Small variant calling, Germline, WGS, WES
Visualization Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
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), nipype, 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
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
Dataset Management Apps
Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
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
Last modified 26d ago
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Contents
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
RNAseq Global Workflows
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