How do I authenticate with DNAnexus using this skill?

The skill provides instructions for installing the dxpy library and using the 'dx login' command to authenticate your session for project and data access.

What is the DNAnexus Integration skill used for?

It helps developers and bioinformaticians build, deploy, and manage genomics applications and data on the DNAnexus cloud platform using the dxpy SDK and command-line tools.

Can I automate batch processing with this skill?

Absolutely. The skill provides code patterns for searching data objects, launching parallel jobs, and orchestrating complex, multi-step analysis workflows.

Does this skill support standard bioinformatics file formats?

Yes, it includes specific patterns and guidance for handling common genomics data types including FASTQ, BAM, and VCF files within the DNAnexus ecosystem.

DNAnexus Genomics Integration

Name: DNAnexus Genomics Integration
Author: Microck

byMicrock

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Data Science & ML

Develops, deploys, and manages genomics pipelines and biomedical data on the DNAnexus cloud platform.

About

This skill integrates the DNAnexus cloud genomics platform with Claude, enabling bioinformaticians and developers to build apps, manage large-scale biomedical data, and orchestrate complex analysis workflows. It provides comprehensive support for the dxpy Python SDK, dxapp.json configuration, and data object management for standard files like FASTQ, BAM, and VCF. Whether you are automating data uploads, monitoring parallel job execution, or configuring Docker-based environments, this skill ensures best practices for scalable, cloud-based genomic research.

Key Features

Programmatic platform access via standardized dxpy SDK patterns
Orchestration of parallel jobs and multi-step bioinformatics workflows
Comprehensive management of genomics data objects, metadata, and projects
81 GitHub stars
App development and deployment using dx-toolkit and Python entry points
Dependency management and Docker integration for reproducible pipelines

Use Cases

Building and testing custom bioinformatics apps for alignment and variant calling
Automating batch processing of sequencing data across multiple cloud projects
Managing large-scale genomics data organization and permission settings via script

About

Key Features

Programmatic platform access via standardized dxpy SDK patterns
Orchestration of parallel jobs and multi-step bioinformatics workflows
Comprehensive management of genomics data objects, metadata, and projects
81 GitHub stars
App development and deployment using dx-toolkit and Python entry points
Dependency management and Docker integration for reproducible pipelines

Use Cases

Building and testing custom bioinformatics apps for alignment and variant calling
Automating batch processing of sequencing data across multiple cloud projects
Managing large-scale genomics data organization and permission settings via script