# Tools List
## Public Tools
### Annotation Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ---------------------------------------------------------------------- | ------------------ | --------------------- | ----------- |
| [SnpEff Annotate](https://platform.dnanexus.com/app/snpeff_annotate) | `snpeff_annotate` | SnpEff | Annotation |
| [SnpSift Annotate](https://platform.dnanexus.com/app/snpsift_annotate) | `snpsift_annotate` | SnpSift | Annotation |
### Data Transfer Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------------------------------- | ---------------------------------- | -------------------------------------------------------------------------------------- | --------------------------------------- |
| [AWS S3 Exporter](https://platform.dnanexus.com/app/aws_platform_to_s3_file_transfer) | `aws_platform_to_s3_file_transfer` | AWS S3 | |
| [AWS S3 Importer](https://platform.dnanexus.com/app/aws_s3_to_platform_files) | `aws_s3_to_platform_files` | AWS S3 | |
| [SRA FASTQ Importer](https://platform.dnanexus.com/app/sra_fastq_importer) | `sra_fastq_importer` | [SRA toolkit fasterq-dump](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump) | Retrieve reads in FASTQ format from SRA |
### DNAseq Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| -------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------- |
| [Original Quality Functionally Equivalent](https://platform.dnanexus.com/app/oqfe) | `oqfe` | A revision of [Functionally Equivalent](https://www.nature.com/articles/s41467-018-06159-4) | WGS, WES- alignment and duplicate marking |
| [GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)](https://platform.dnanexus.com/app/gatk4_bqsr_parallel) | `gatk4_bqsr_parallel` | GATK4 - [BaseRecalibrator](https://gatk.broadinstitute.org/hc/en-us/articles/360046222991-BaseRecalibrator) and [ApplyBQSR](https://gatk.broadinstitute.org/hc/en-us/articles/360046222011-ApplyBQSR) | Variant calling |
| [BWA-MEM FASTQ Read Mapper](https://platform.dnanexus.com/app/bwa_mem_fastq_read_mapper) | `bwa_mem_fastq_read_mapper` | BWA-MEM | Short read alignment |
| [GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)](https://platform.dnanexus.com/app/gatk4_haplotypecaller_parallel) | `gatk4_haplotypecaller_parallel` | [GATK4- HaplotypeCaller module](https://gatk.broadinstitute.org/hc/en-us/articles/360045799892-HaplotypeCaller) | Variant calling, post-alignment QC |
| [GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)](https://platform.dnanexus.com/app/gatk4_genotypegvcfs_single_sample_parallel) | `gatk4_genotypegvcfs_single_sample_parallel` | [GATK4- GenotypeGVCFs module](https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs) | Variant calling |
| [Picard MarkDuplicates Mappings Deduplicator](https://platform.dnanexus.com/app/picard_mark_duplicates) | `picard_mark_duplicates` | [MarkDuplicates from the Picard suite of tools](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) | Variant Calling- remove duplicates, post-alignment |
### GWAS Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| --------------------------------------------------------------------------------------------------------- | ----------------------- | ---------------------------------------------- | --------------------------------------------- |
| [REGENIE](https://platform.dnanexus.com/app/regenie) | `regenie` | REGENIE | GWAS |
| [PLINK GWAS](https://platform.dnanexus.com/app/plink_gwas) | `plink_gwas` | PLINK2 |
|
| [Raremetal2 - Raremetal and Raremetalworker](https://platform.dnanexus.com/app/raremetal2) | `raremetal2` | Raremetalworker, Raremetal | Meta-analysis of rare variants |
| [SAIGE GWAS - Gene and region based association tests](https://platform.dnanexus.com/app/saige_gwas_gbat) | `saige_gwas_gbat` | [SAIGE](https://saigegit.github.io/SAIGE-doc/) | Gene and region-based association tests |
| [SAIGE GWAS - Single variant association tests](https://platform.dnanexus.com/app/saige_gwas_svat) | `saige_gwas_svat` | [SAIGE](https://saigegit.github.io/SAIGE-doc/) | Single variant association tests |
| [SAIGE GWAS GRM](https://platform.dnanexus.com/app/saige_gwas_grm) | `saige_gwas_grm` | [SAIGE](https://saigegit.github.io/SAIGE-doc/) | Null model fitting using a GRM for SAIGE GWAS |
| [SAIGE-GWAS Sparse GRM](https://platform.dnanexus.com/app/saige_gwas_sparse_grm) | `saige_gwas_sparse_grm` | [SAIGE](https://saigegit.github.io/SAIGE-doc/) | Sparse GRM construction for SAIGE GWAS |
| [PLINK GWAS Pipeline](https://platform.dnanexus.com/app/plink_pipeline) | `plink_pipeline` | Plink2 | |
| [PLATO GWAS Pipeline](https://platform.dnanexus.com/app/plato_pipeline) | `plato_pipeline` | Plato, Plink2 | |
| [LocusZoom](https://platform.dnanexus.com/app/locuszoom) | `locuszoom` | LocusZoom | GWAS, visualization |
### File Transfer Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------ | ------------- | --------------------- | ---------------------------------------------------- |
| [URL Fetcher](https://platform.dnanexus.com/app/url_fetcher) | `url_fetcher` | N/A | Fetches a file from a URL onto the DNAnexus Platform |
### Imaging Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| -------------------------------------------------------------------------------------- | ------------------------- | ---------------------------------------------------------------------------------------------------------- | ------------------------------------ |
| [Imaging Multitool - MONAI](https://platform.dnanexus.com/app/imaging_multitool_monai) | `imaging_multitool_monai` | [MONAI Core](https://github.com/Project-MONAI/MONAI) | Image processing |
| [3D Slicer](https://platform.dnanexus.com/app/3d_slicer) | `3d_slicer` | [3D Slicer](https://github.com/Slicer/Slicer) | Visualization and image analysis |
| [3D Slicer with MONAI Label](https://platform.dnanexus.com/app/3d_slicer_monai) | `3d_slicer_monai` | [3D Slicer](https://github.com/Slicer/Slicer), [MONAI Label](https://github.com/Project-MONAI/MONAILabel/) | Interactive radiology image analysis |
### Import Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| -------------------------------------------------------------------------- | -------------------- | ------------------------------------------------------------------------------------- | ---------------------------------------------------- |
| [SRA FASTQ Importer](https://platform.dnanexus.com/app/sra_fastq_importer) | `sra_fastq_importer` | [SRA tools: fasterq-dump](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump) | Retrieve reads in FASTQ format from SRA |
| [URL Fetcher](https://platform.dnanexus.com/app/url_fetcher) | `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](https://platform.dnanexus.com/app/cloud_workstation) | `cloud_workstation` | N/A | SSH-accessible Unix shell on a Platform cloud worker. Use it for on-demand analysis of Platform data. |
| [ttyd](https://platform.dnanexus.com/app/ttyd) | `ttyd` | N/A | Unix shell on a Platform cloud worker in your browser. Use it for on-demand CLI operations and to launch httpsApp-enabled apps or applets on 2 extra ports |
### Joint Genotyping Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ---------------------------------------------------- | ----------- | --------------------- | ------------------------------------------------------------------------- |
| [GLnexus](https://platform.dnanexus.com/app/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 |
| ----------------------------------------------------------------------------- | ---------------- | --------------------------------------------------------------------- | ------------------------------------------ |
| [SAMtools Mappings Indexer](https://platform.dnanexus.com/app/samtools_index) | `samtools_index` | [SAMtools](https://www.htslib.org/doc/samtools.html) - SAMtools index | Building BAM index file |
| [SAMtools Mappings Sorter](https://platform.dnanexus.com/app/samtools_sort) | `samtools_sort` | [SAMtools](https://www.htslib.org/doc/samtools.html) - SAMtools sort | Sort alignment result based on coordinates |
### PheWAS Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ---------------------------------------------------- | ----------- | --------------------- | ----------- |
| [PHESANT](https://platform.dnanexus.com/app/phesant) | `phesant` | PHESANT | PheWAS |
### PRS Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ----------------------------------------------------- | ----------- | --------------------- | --------------------- |
| [PRSice 2](https://platform.dnanexus.com/app/prsice2) | `prsice2` | PRSice-2 | Polygenic risk scores |
### QC Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------------------ | ----------------- | ----------------------------------------------- | ----------------------------------------- |
| [MultiQC](https://platform.dnanexus.com/app/multiqc) | `multiqc` | MultiQC | QC reporting |
| [Qualimap2 Analysis](https://platform.dnanexus.com/app/qualimap2_anlys) | `qualimap2_anlys` | Qualimap2 | QC |
| [RNASeQC](https://platform.dnanexus.com/app/rnaseqc) | `rnaseqc` | [RNASeQC 2](https://github.com/getzlab/rnaseqc) | Transcriptomics Expression Quantification |
| [FastQC Reads Quality Control](https://platform.dnanexus.com/app/fastqc) | `fastqc` | FastQC |
|
### Quantification Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------------------------------------- | ---------------------- | --------------------- | ----------------------------------------- |
| [Salmon Quantification](https://platform.dnanexus.com/app/salmon_quant) | `salmon_quant` | Salmon | Transcriptomics Expression Quantification |
| [Salmon Mapping and Quantification](https://platform.dnanexus.com/app/salmon_mapping_quant) | `salmon_mapping_quant` | Salmon | Transcriptomics Expression Quantification |
### Read Mapping Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| --------------------------------------------------------------------------------------------------------------------------- | ---------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------- |
| [Bowtie2 FASTA Indexer](https://web.archive.org/web/20240725171403/https://platform.dnanexus.com/app/bowtie2_fasta_indexer) | `bowtie2_fasta_indexer` | `bowtie2`: `bowtie2-build` | Building reference for Bowite2 alignment |
| [Bowtie2 FASTQ Read Mapper](https://platform.dnanexus.com/app/bowtie2_fastq_read_mapper) | `bowtie2_fastq_read_mapper` | `bowtie2`, SAMtools view, SAMtools sort, SAMtools index | Short read alignment |
| [BWA FASTA Indexer](https://platform.dnanexus.com/app/bowtie2_fasta_indexer) | `bwa_fasta_indexer` | BWA- bwa index | Building reference for BWA alignment |
| [BWA-MEM FASTQ Read Mapper](https://platform.dnanexus.com/app/bwa_mem_fastq_read_mapper) | `bwa_mem_fastq_read_mapper` | BWA-MEM | Short read alignment |
| [STAR Generate Genome Index](https://platform.dnanexus.com/app/star_generate_genome_index) | `star_generate_genome_index` | [STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) (`--runMode genomeGenerate`) | RNA Seq- indexing |
| [STAR Mapping](https://platform.dnanexus.com/app/star_mapping) | `star_mapping` | [STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) | RNA Seq- mapping |
| [Subread featureCounts](https://platform.dnanexus.com/app/subread_feature_counts) | `subread_feature_counts` | featureCounts | Read summarization, RNAseq |
| [Salmon Index Builder](https://web.archive.org/web/20240725171403/https://platform.dnanexus.com/app/salmon_index_builder) | `salmon_index_builder` | Salmon | Transcriptomics Expression Quantification |
| [Salmon Mapping and Quantification](https://platform.dnanexus.com/app/salmon_mapping_quant) | `salmon_mapping_quant` | Salmon | Transcriptomics Expression Quantification |
### Read Manipulation Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------------------------------------------------------------- | ---------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------- |
| [GATK4 Base Quality Score Recalibrator (Parallel Per-Chrom)](https://platform.dnanexus.com/app/gatk4_bqsr_parallel) | `gatk4_bqsr_parallel` | \[GATK4 - [BaseRecalibrator](https://gatk.broadinstitute.org/hc/en-us/articles/360046222991-BaseRecalibrator) and [ApplyBQSR](https:/gatk.broadinstitute.org/hc/en-us/articles/360046222011-ApplyBQSR) | Variant calling |
| [Flexbar FASTQ Read Trimmer](https://platform.dnanexus.com/app/flexbar_fastq_read_trimmer) | `flexbar_fastq_read_trimmer` | [`flexbar`](https://github.com/seqan/flexbar/wiki) | QC |
| [Trimmomatic](https://platform.dnanexus.com/app/trimmomatic) | `trimmomatic` | [`trimmomatic`](https://github.com/usadellab/Trimmomatic) | Read quality trimming, adapter trimming |
### RNAseq Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------------------------------------------------------------------- | ---------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------- |
| [RNASeQC](https://platform.dnanexus.com/app/rnaseqc) | `rnaseqc` | [RNASeQC 2](https://github.com/getzlab/rnaseqc) | Transcriptomics Expression Quantification |
| [STAR Generate Genome Index](https://platform.dnanexus.com/app/star_generate_genome_index) | `star_generate_genome_index` | [STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) (`--runMode genomeGenerate`) | RNA Seq- indexing |
| [STAR Mapping](https://platform.dnanexus.com/app/star_mapping) | `star_mapping` | [STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) | RNA Seq- mapping |
| [Subread featureCounts](https://platform.dnanexus.com/app/subread_feature_counts) | `subread_feature_counts` | featureCounts | Read summarization, RNAseq |
| [STAR Generate Genome Index](https://platform.dnanexus.com/app/star_generate_genome_index) | `star_generate_genome_index` | [STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) (`--runMode genomeGenerate`) | Transcriptomics Expression Quantification |
| [STAR Mapping](https://platform.dnanexus.com/app/star_mapping) | `star_mapping` | [STAR](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (Spliced Transcripts Alignment to a Reference) | Transcriptomics Expression Quantification |
| [Salmon Index Builder](https://web.archive.org/web/20240725171403/https://platform.dnanexus.com/app/salmon_index_builder) | `salmon_index_builder` | Salmon | Transcriptomics Expression Quantification |
| [Salmon Mapping and Quantification](https://platform.dnanexus.com/app/salmon_mapping_quant) | `salmon_mapping_quant` | Salmon | Transcriptomics Expression Quantification |
| [Salmon Quantification](https://platform.dnanexus.com/app/salmon_quant) | `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](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb) | Transcript\_Expression\_Part-02\_Analysis-diff-exp\_R.ipynb | DESeq2 | |
| [Transcript\_Expression\_Part-03\_Analysis-GSEA\_R.ipynb](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb) | Transcript\_Expression\_Part-03\_Analysis-GSEA\_R.ipynb | WebGestaltR | |
| [Transcript\_Expression\_Part-04\_Analysis-CoEx-Network\_R.ipynb](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb) | Transcript\_Expression\_Part-04\_Analysis-CoEx-Network\_R.ipynb | WGCNA, topGO | |
| [Transcript\_Expression\_Part-05\_Analysis-Regulatory-Network\_R.ipynb](https://github.com/dnanexus/OpenBio/blob/master/transcriptomics/tutorial_notebooks/Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb) | Transcript\_Expression\_Part-05\_Analysis-Regulatory-Network\_R.ipynb | GENIE3 | |
### Utility Apps
| Name of Tool | Name in CLI | Scientific Algorithm | Common Uses |
| ------------------------------------------------------------------------ | ------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
| [File Concatenator](https://platform.dnanexus.com/app/file_concatenator) | `file_concatenator` | N/A | |
| [Gzip File Compressor](https://platform.dnanexus.com/app/gzip) | `gzip` | gzip | |
| [Swiss Army Knife](https://platform.dnanexus.com/app/swiss-army-knife) | `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](https://platform.dnanexus.com/app/ttyd) | `ttyd` | N/A | Unix shell on a platform cloud worker in your browser. Use it for on-demand CLI operations and to launch httpsApp-enabled apps or applets on 2 extra ports |
### Variant Calling Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| -------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------- |
| [CNVkit](https://platform.dnanexus.com/app/cnvkit_batch) | `cnvkit_batch` | [CNVkit](https://cnvkit.readthedocs.io/en/stable/) | Copy Number Variant |
| [GATK4 HaplotypeCaller (Parallel Per-IntervalByNs)](https://platform.dnanexus.com/app/gatk4_haplotypecaller_parallel) | `gatk4_haplotypecaller_parallel` | [GATK4- HaplotypeCaller module](https://gatk.broadinstitute.org/hc/en-us/articles/360045799892-HaplotypeCaller) | Variant calling, post-alignment QC |
| [GATK4 Single-Sample GenotypeGVCFs (Parallel Per-Chrom)](https://platform.dnanexus.com/app/gatk4_genotypegvcfs_single_sample_parallel) | `gatk4_genotypegvcfs_single_sample_parallel` | [GATK4- GenotypeGVCFs module](https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs) | Variant calling |
| [Picard MarkDuplicates Mappings Deduplicator](https://platform.dnanexus.com/app/picard_mark_duplicates) | `picard_mark_duplicates` | [MarkDuplicates from the Picard suite of tools](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) | Variant Calling- remove duplicates, post-alignment |
| [FreeBayes Variant Caller](https://platform.dnanexus.com/app/freebayes) | `freebayes` | [FreeBayes](https://github.com/freebayes/freebayes/blob/master/README.md) | Use for short variant calls |
| [GATK4 Mutect2 Variant Caller and Filter](https://platform.dnanexus.com/app/gatk4_mutect2_variant_caller_and_filter) | `gatk4_mutect2_variant_caller_and_filter` | [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2) | Somatic variant calling and post calling filtering |
| [GATK4 Somatic Panel Of Normals Builder](https://platform.dnanexus.com/app/gatk4_somatic_panel_of_normals_builder) | `gatk4_somatic_panel_of_normals_builder` | [GATK CreateSomaticPanelOfNormals](https://gatk.broadinstitute.org/hc/en-us/articles/5358921041947-CreateSomaticPanelOfNormals-BETA) | 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](https://platform.dnanexus.com/app/locuszoom) | `locuszoom` | LocusZoom | GWAS, visualization |
## Titan Tools
{% hint style="info" %}
A Titan license is required to access and use these tools. Contact [DNAnexus Sales](mailto:sales@dnanexus.com) for more information.
{% endhint %}
### Statistics Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ----------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| [JupyterLab with ML](https://platform.dnanexus.com/app/dxjupyterlab) | `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 |
| [JupyterLab with Python\_R](https://platform.dnanexus.com/app/dxjupyterlab) | `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 |
| [JupyterLab with Stata](https://platform.dnanexus.com/app/dxjupyterlab) | `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 |
| [JupyterLab with IMAGE\_PROCESSING](https://platform.dnanexus.com/app/dxjupyterlab) | `dxjupyterlab` | `dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `nipype`, `freesurfer`, `FSL` | Running imaging processing related analysis |
| [JupyterLab with MONAI\_ML](https://platform.dnanexus.com/app/dxjupyterlab) | `dxjupyterlab` | `dxpy`, `matplotlib`, `numpy`, `pandas`, `papermill`, `scipy`, `seaborn`, `dxdata`, `keras`, `scikit-learn`, `TensorFlow`, `torch`, `monai`, `monailabel`, `3D Slicer` | Running image processing related analysis, building and testing models and algorithms in an interactive way |
## Apollo Tools
{% hint style="info" %}
An Apollo license is required to access and use these tools. Contact [DNAnexus Sales](mailto:sales@dnanexus.com) for more information.
{% endhint %}
### Dataset Administration Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| --------------------------------------------------------------------------- | ---------------------- | --------------------- | ----------------- |
| [Data Model Loader](https://platform.dnanexus.com/app/data_model_loader_v2) | `data_model_loader_v2` | Dataset Creation | Dataset Creation |
| [Dataset Extender](https://platform.dnanexus.com/app/dataset-extender) | `dataset-extender` | Dataset Extension | Dataset Extension |
### Dataset Management Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ---------------------------------------------------------------------- | ------------------ | --------------------- | --------------------- |
| [CSV Loader](https://platform.dnanexus.com/app/csv-loader) | `csv-loader` | N/A | Data Loading |
| [Spark SQL Runner](https://platform.dnanexus.com/app/spark-sql-runner) | `spark-sql-runner` | Spark SQL | Dynamic SQL Execution |
| [Table Exporter](https://platform.dnanexus.com/app/table-exporter) | `table-exporter` | N/A | Data Extraction |
### Data Science Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| -------------------------------------------------------------------------------------------------------------- | ---------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------- |
| [JupyterLab with Spark Cluster with Glow](https://platform.dnanexus.com/panx/tools/workers/jupyterLab) | `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 |
| [JupyterLab with Spark Cluster with Hail](https://platform.dnanexus.com/panx/tools/workers/jupyterLab) | `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 |
| [JupyterLab with Spark Cluster with Hail and VEP](https://platform.dnanexus.com/panx/tools/workers/jupyterLab) | `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 somatic FASTQ to VCF](https://platform.dnanexus.com/app/sentieon-tnseq) | `sentieon-tnseq` | Sentieon's FASTQ to VCF somatic analysis pipeline | WGS, WES, accelerated analysis |
| [Sentieon BWA-MEM and Sentieon De-duplication](https://platform.dnanexus.com/app/sentieon-bwa) | `sentieon-bwa` | Sentieon's FASTQ to BAM/CRAM pipeline | WGS, WES, accelerated analysis |
| [Germline Pipeline (NVIDIA Clara Parabricks accelerated)](https://platform.dnanexus.com/app/pbgermline) | `pbgermline` | BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration | WGS, WES, accelerated analysis |
| [Sentieon somatic BAM/CRAM to VCF](https://platform.dnanexus.com/app/sentieon-tnbam) | `sentieon-tnbam` | Sentieon's BAM to VCF somatic analysis pipeline | WGS, WES, accelerated analysis |
| [DeepVariant Pipeline (Parabricks accelerated)](https://platform.dnanexus.com/app/pbdeepvariant) | `pbdeepvariant` | Deepvariant | Variant calling, accelerated analysis |
| [Sentieon UMI](https://platform.dnanexus.com/app/sentieon-umi) | `sentieon-umi` | Sentieon's pre-processing and alignment pipeline for next-generation sequence | WGS, WES, accelerated analysis |
| [Sentieon germline BAM/CRAM to VCF](https://platform.dnanexus.com/app/sentieon-dnabam) | `sentieon-dnabam` | Sentieon's BAM to VCF germline analysis pipeline | WGS, WES, accelerated analysis |
| [Sentieon distributed Joint Genotyping](https://platform.dnanexus.com/app/sentieon-joint_genotyping) | `sentieon-joint_genotyping` | Sentieon GVCFtyper | WGS, WES, accelerated analysis |
| [Sentieon Functional equivalent protocol](https://platform.dnanexus.com/app/sentieon-ccdg) | `sentieon-ccdg` | Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline | WGS, WES, accelerated analysis |
| [Sentieon germline FASTQ to VCF](https://platform.dnanexus.com/app/sentieon-dnaseq) | `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 distributed Joint Genotyping](https://platform.dnanexus.com/app/sentieon-joint_genotyping) | `sentieon-joint_genotyping` | Sentieon GVCFtyper | WGS, WES, accelerated analysis |
### Read Mapping Apps
| Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
| ------------------------------------------------------------------------------------------------------- | ----------------- | ----------------------------------------------------------------------------------------------- | ------------------------------------- |
| [Sentieon somatic FASTQ to VCF](https://platform.dnanexus.com/app/sentieon-tnseq) | `sentieon-tnseq` | Sentieon's FASTQ to VCF somatic analysis pipeline | WGS, WES, accelerated analysis |
| [Sentieon BWA-MEM and Sentieon De-duplication](https://platform.dnanexus.com/app/sentieon-bwa) | `sentieon-bwa` | Sentieon's FASTQ to BAM/CRAM pipeline | WGS, WES, accelerated analysis |
| [Germline Pipeline (NVIDIA Clara Parabricks accelerated)](https://platform.dnanexus.com/app/pbgermline) | `pbgermline` | BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration | WGS, WES, accelerated analysis |
| [DeepVariant Pipeline (Parabricks accelerated)](https://platform.dnanexus.com/app/pbdeepvariant) | `pbdeepvariant` | Deepvariant | Variant calling, accelerated analysis |
| [Sentieon UMI](https://platform.dnanexus.com/app/sentieon-umi) | `sentieon-umi` | Sentieon's pre-processing and alignment pipeline for next-generation sequence | WGS, WES, accelerated analysis |
| [Sentieon Functional equivalent protocol](https://platform.dnanexus.com/app/sentieon-ccdg) | `sentieon-ccdg` | Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline | WGS, WES, accelerated analysis |
| [Sentieon germline FASTQ to VCF](https://platform.dnanexus.com/app/sentieon-dnaseq) | `sentieon-dnaseq` | Sentieon's FASTQ to VCF germline analysis pipeline | WGS, WES, accelerated analysis |
---
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