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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
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
​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
​Regenie​
regenie
REGENIE
GWAS
plink_gwas
PLINK2
raremetal2
RAREMETALWORKER, RAREMETAL
saige_gwas_gbat
​SAIGE​
saige_gwas_svat
​SAIGE​
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
hisat2_index
Transcriptomics
hisat2_mapper
Transcriptomics
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
gatk4_bqsr_parallel
Variant calling
flexbar_fastq_read_trimmer
​Flexbar​
QC
trimmomatic
Read quality trimming, adapter trimming

RNAseq Apps

Name of Tool
Name in CLI
Scientific Algorithms
Common Uses
star_fusion_caller
RNA-Seq fusion calling
gatk4_haplotypecaller_rnaseq
​GATK best practice workflow for RNAseq short variant discovery (SNPs + Indels)(SplitNCigarReads, HaplotypeCaller, VariantFiltration)
RNA-seq variant calling, post-alignment QC
​RNASeQC​
rnaseqc
​RNAseqC 2​
Transcriptomics Expression Quantification
rseqc_rna_bam_eval
RSeQC
Transcriptomics Expression Quantification
hisat2_index
Transcriptomics
hisat2_mapper
Transcriptomics
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
star_fusion_caller
RNA-Seq fusion calling
gatk4_haplotypecaller_rnaseq
​GATK best practice workflow for RNAseq short variant discovery (SNPs + Indels)(SplitNCigarReads, HaplotypeCaller, VariantFiltration)
RNA-seq variant calling, post-alignment QC
​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
gatk4_mutect2_variant_caller_and_filter
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.

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,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