Tools List

Public Tools

Annotation Apps

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
snpeff_annotate
SnpEff
Annotation
snpsift_annotate
SnpSift
Annotation
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 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
A revision of Functionally Equivalent
WGS, WES- alignment and duplicate marking
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
Strelka2
Small variant calling, Germline, WGS, WES
strelka2_somatic
Strelka2
Small variant calling, Somatic analysis

GWAS Apps

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
plink_gwas
PLINK2
raremetal2
RAREMETALWORKER, RAREMETAL
saige_gwas_grm
SAIGE
saige_gwas_sparse_grm
SAIGE
plink_pipeline
Plink2
plato_pipeline
Plato, Plink2
LocusZoom
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
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
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_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_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

Quantification Apps

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
rsem
RSEM
Transcriptomics Expression Quantification
kallisto
Kallisto
Transcriptomics Expression Quantification
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_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- 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
star_generate_genome_index
STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)
RNA Seq- indexing
star_mapping
STAR (Spliced Transcripts Alignment to a Reference)
RNA Seq- mapping
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 (Spliced Transcripts Alignment to a Reference)
Transcriptomics Expression Quantification
salmon_index_builder
Salmon
Transcriptomics Expression Quantification
salmon_mapping_quant
Salmon
Transcriptomics Expression Quantification

Read Manipulation Apps

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
flexbar_fastq_read_trimmer
Flexbar
QC
trimmomatic
Read quality trimming, adapter trimming

RNAseq Apps

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
star_generate_genome_index
STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)
RNA Seq- indexing
star_mapping
STAR (Spliced Transcripts Alignment to a Reference)
RNA Seq- mapping
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 (Spliced Transcripts Alignment to a Reference)
Transcriptomics Expression Quantification
salmon_index_builder
Salmon
Transcriptomics Expression Quantification
salmon_mapping_quant
Salmon
Transcriptomics Expression Quantification
kallisto_index_builder
Kallisto
Transcriptomics Expression Quantification
rsem
RSEM
Transcriptomics Expression Quantification
kallisto
Kallisto
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

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
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
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

Variant Calling Apps

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
CNVkit
cnvkit_batch
CNVkit
Copy Number Variant
deepvariant_germline
Variant calling
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
Strelka2
Small variant calling, Germline, WGS, WES
strelka2_somatic
Strelka2
Small variant calling, Somatic analysis
freebayes
FreeBayes
Use for short variant calls

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
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
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