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

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

Small variant calling, Germline, WGS, WES

strelka2_somatic

Small variant calling, Somatic analysis

GWAS Apps

Name of Tool

Name in CLI

Scientific Algorithms

Common Uses

regenie

REGENIE

GWAS

plink_gwas

PLINK2

raremetal2

RAREMETALWORKER, RAREMETAL

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

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

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

rseqc_rna_bam_eval

RSeQC

Transcriptomics Expression Quantification

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

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

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

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

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_batch

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

Small variant calling, Germline, WGS, WES

strelka2_somatic

Small variant calling, Somatic analysis

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

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

Last updated

Copyright 2024 DNAnexus