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
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