DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT OVERVIEWBLOGCHARGE PROJECT The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.

DNANEXUS

View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

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Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

DNANEXUS

Come work with us! View open positions with our team.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_job_id (dxid): """:param dxid: ID of a job:type dxid: string Sets the ID of the running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment, but wish to test it outside of an actual Execution Environment. """ global JOB_ID JOB_ID = DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT OVERVIEWBLOGCHARGE PROJECT The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.

DNANEXUS

View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

DNANEXUS

Come work with us! View open positions with our team.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_job_id (dxid): """:param dxid: ID of a job:type dxid: string Sets the ID of the running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment, but wish to test it outside of an actual Execution Environment. """ global JOB_ID JOB_ID =

DNANEXUS

View our products for multi-omics data exploration and NGS analysis DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform through

DNANEXUS

Come work with us! View open positions with our team.

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Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the US DASH EXAMPLE WEB APP This is an example web app made with Dash, which in turn uses Flask underneath. View full source code on GitHub COMPARISON OF BGISEQ 500 TO ILLUMINA NOVASEQ DATA Comparison of BGISEQ 500 to Illumina NovaSeq Data. Last Thursday, BGI uploaded three WGS data sets of NA12878/HG001. Included in this was a challenge to conduct a side-by-side analysis. Albert Villela of Cambridge Epigenetix drew our attention to this dataset. Given our love of benchmarking and new technologies, we applied our evaluation SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are

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DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.

DNANEXUS

View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.

DNANEXUS

View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

DNANEXUS

Come work with us! View open positions with our team.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_job_id (dxid): """:param dxid: ID of a job:type dxid: string Sets the ID of the running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment, but wish to test it outside of an actual Execution Environment. """ global JOB_ID JOB_ID =

DNANEXUS

View our products for multi-omics data exploration and NGS analysis DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform through

DNANEXUS

Come work with us! View open positions with our team. HUMAN REFERENCE GENOMES The Human Genome Project set out to identify the sequences of these 25 distinct DNA entities (chromosomes 1 through 22, chromosomes X and Y, and the mitochondria), aka "the human genome". In February of 2009, the Genome Reference Consortium (GRC) released "build 37" of the human genome, called GRCh37.In 2013, the GRC released a newer "build 38" of the human genome, called GRCh38. GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the US

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Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

ASSOCIATION BROWSER

Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation

(Manhattan

DASH EXAMPLE WEB APP This is an example web app made with Dash, which in turn uses Flask underneath. View full source code on GitHub SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

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DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the

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Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

VCF PREPROCESSING

The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

VCF PREPROCESSING

The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform through

DNANEXUS

We're building a world-class team of innovators to harness cutting-edge science to solve the future's most important data problems in precision medicine.

DNANEXUS

Come work with us! View open positions with our team.

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Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

EOL DOCUMENTATION

End-of-life (EOL) documentation for products and tools that are no longer supported will be linked from the menu on the left.

SINGLE SIGN-ON

To use the command line with an SSO-enabled account, first create an API token on the DNAnexus Platform website. Click on the user name and navigate to the Profile, then click API Tokens and create a new token. Then specify the token on the command line using dx login --token TOKEN. How do users register their SSO accounts on DNAnexus for the GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the US

ASSOCIATION BROWSER

Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation

(Manhattan

SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUS

INCDNANEXUS REVENUE

Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

VCF PREPROCESSING

The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUS

INCDNANEXUS REVENUE

Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

VCF PREPROCESSING

The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform through

DNANEXUS

We're building a world-class team of innovators to harness cutting-edge science to solve the future's most important data problems in precision medicine.

DNANEXUS

Come work with us! View open positions with our team.

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

EOL DOCUMENTATION

End-of-life (EOL) documentation for products and tools that are no longer supported will be linked from the menu on the left.

SINGLE SIGN-ON

To use the command line with an SSO-enabled account, first create an API token on the DNAnexus Platform website. Click on the user name and navigate to the Profile, then click API Tokens and create a new token. Then specify the token on the command line using dx login --token TOKEN. How do users register their SSO accounts on DNAnexus for the GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the US

ASSOCIATION BROWSER

Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation

(Manhattan

SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT

OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUS

INCDNANEXUS REVENUE

Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the

LOADING PLATFORM...

Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.

VCF PREPROCESSING

The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of the

container, /opt

SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000

individuals.

COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

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OVERVIEWBLOGCAREERS

The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUS

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Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.

AUTHENTICATION

Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the

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VCF PREPROCESSING

The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform through

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EOL DOCUMENTATION

End-of-life (EOL) documentation for products and tools that are no longer supported will be linked from the menu on the left.

SINGLE SIGN-ON

To use the command line with an SSO-enabled account, first create an API token on the DNAnexus Platform website. Click on the user name and navigate to the Profile, then click API Tokens and create a new token. Then specify the token on the command line using dx login --token TOKEN. How do users register their SSO accounts on DNAnexus for the GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the US

ASSOCIATION BROWSER

Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation

(Manhattan

SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speed

up your tasks.

DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are ; WE'RE SORRY BUT DNA-NEXUS DOESN'T WORK PROPERLY WITHOUT JAVASCRIPT ENABLED. PLEASE ENABLE IT TO CONTINUE.

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* DNAnexus Apollo™Multi-omics Data Science Exploration, Analysis &

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* DNAnexus Titan™Next-Generation Sequencing Data Analysis * DNAnexus Portals™Customized, Private & Collaborative Environments * DNAnexus GxP SupportRegulatory & Quality Services for Clinical, Manufacturing, & Laboratory Practices

USE CASES

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INDUSTRY

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PRODUCTS

* Products Overview

* DNAnexus Apollo™ Multi-omics Data Science Exploration, Analysis & Discovery

* DNAnexus Titan™

Next-Generation Sequencing Data Analysis * DNAnexus Portals™ Customized, Private & Collaborative Environments * DNAnexus GxP Support Regulatory & Quality Services for Clinical, Manufacturing, & Laboratory Practices

USE CASES

* Translational Informatics * Population Genomics

* Genomic Analysis

* Clinical Trials

* Clinical Diagnostics * Molecular Pathology

INDUSTRY

* Pharmaceutical & Biotech * Diagnostic Test Providers * Sequencing Service Providers * Academic Core Labs

* Genome Centers

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Dedicated

to enabling

precision

medicine.

DNANEXUS® has built the world’s most secure, trusted cloud platform and global network for scientific collaboration and accelerated discovery. We partner with customers to tackle the world’s most exciting opportunities in human health and beyond.

ENABLING PROGRESS

1Powerful & Purpose-Built Platform Rapid, Scalable & Secure Data Science Using genomics in the discovery and development of new medicines and diagnostics requires the ability to manage high volumes of data in a secure, compliant, production-ready environment. DNAnexus provides a platform that facilitates the integration of the genetic data with other data types and enables collaboration globally. 2A True Global Network Connecting Pharmaceutical, Medical Centers & Research Partners Progress in science and medicine accelerates when researchers collaborate around responsibly shared datasets. As the complexity and scale of data increases, collaboration becomes more difficult to manage. DNAnexus enables distributed research teams access to the same data and analysis tools to advance scientific discovery. 3Move Beyond Genomics Extract Knowledge from Diverse Data Insights from genomic data are revealed more often when multiple data types are analyzed together. DNAnexus helps advance medical discovery by bringing genomic, multi-omics, and clinical data securely together on a single scalable platform.

ENABLING DISCOVERY

LATEST NEWS, CASE STUDIES, WHITE PAPERS, WEBINARS & MORE. Sign up for our monthly newsletter to learn about DNAnexus initiatives and gain exclusive access to new tools and product

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Case StudyDNAnexus Supports Data Management & Genomic Analysis for a Global Research Consortium Case StudyHow One Pharma Company Advanced Their Drug Discovery &

Development Process

Case StudyRapid Whole-Genome Sequencing Decreases Infant Morbidity and Cost of Hospitalization VideoPipeline Evolution at Regeneron Genetics Center ENABLING COLLABORATIVE SCIENCE In collaboration with Microsoft, DNAnexus Portals™

forms the

foundation of St. Jude Cloud, providing researchers access to the world’s largest public repository of pediatric cancer genomic data to accelerate data mining, analysis, and visualization capabilities.

Read More

Vertebrate Genomes Project leverages DNAnexus Titan™

to achieve their

ambitious goal of generating reference quality genome assemblies of all 66,000 extant vertebrate species.Read More DNAnexus is proud to power precisionFDA , a community platform for next-generation sequencing assay evaluation and regulatory science exploration.Read More

ENABLING INNOVATION

We cultivate a culture of constant improvement in science & technology. Our xVantage Group is dedicated to helping you realize

your goals.

Meet the Team

"The best thing you can do with DNAnexus is give them a problem to

solve."

JEFFREY REID

Executive Director, Head of Genome Informatics Regeneron Genetics Center "Collaboration is vital to advancing scientific discovery. We are excited to partner with Microsoft and DNAnexus to create infrastructure and tools to share data and accelerate progress toward finding cures for pediatric cancer and other life-threatening

diseases."

JAMES R. DOWNING

President & CEO

St. Jude Children's Research Hospital

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