Is this suitable for large-scale sequencing data?

Yes, it is designed to handle common bioinformatics formats like FASTQ, BAM, and VCF, offering patterns for batch processing and project organization.

Does it support Docker and custom tool configuration?

Absolutely. The skill provides guidance on configuring dxapp.json, managing system dependencies, and integrating Docker containers for complex environments.

What is the DNAnexus Integration skill for Claude?

It is a specialized capability that provides Claude with the domain knowledge to help developers build, deploy, and manage bioinformatics tools and data on the DNAnexus cloud platform.

Can this skill help me write dxpy Python scripts?

Yes, it includes comprehensive patterns and references for the dxpy Python SDK to automate file uploads, job launches, and data searches.

How do I authenticate with DNAnexus when using this skill?

The skill provides instructions for using the 'dx login' command to authenticate your session, ensuring Claude can help you manage your projects and data securely.

DNAnexus Genomics Integration

Name: DNAnexus Genomics Integration
Author: Microck

byMicrock

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Cloud Infrastructure

Facilitates the development, deployment, and management of bioinformatics pipelines on the DNAnexus cloud genomics platform.

About

This skill empowers Claude to act as a specialized assistant for the DNAnexus platform, a leading environment for biomedical data analysis. It provides comprehensive support for building custom apps and applets, managing large-scale genomic data objects, orchestrating complex workflows, and utilizing the dxpy Python SDK. Whether you are automating file uploads, configuring dxapp.json for Docker-based pipelines, or monitoring parallel job execution, this skill offers the specific patterns and best practices needed to streamline bioinformatics development and data science operations.

Key Features

Standardized patterns for batch processing and multi-step analysis pipelines.
Streamlined workflow orchestration and job monitoring via the dxpy Python SDK.
Automated DNAnexus app and applet development using dx-app-wizard patterns.
Advanced configuration support for dxapp.json, including dependency and Docker management.
Comprehensive data management for genomic files including FASTQ, BAM, and VCF.
81 GitHub stars

Use Cases

Building and deploying production-grade variant calling or alignment pipelines.
Scaling bioinformatics analyses through parallel job execution and subjob management.
Automating the organization and metadata tagging of sequencing data across projects.

About

Key Features

Standardized patterns for batch processing and multi-step analysis pipelines.
Streamlined workflow orchestration and job monitoring via the dxpy Python SDK.
Automated DNAnexus app and applet development using dx-app-wizard patterns.
Advanced configuration support for dxapp.json, including dependency and Docker management.
Comprehensive data management for genomic files including FASTQ, BAM, and VCF.
81 GitHub stars

Use Cases

Building and deploying production-grade variant calling or alignment pipelines.
Scaling bioinformatics analyses through parallel job execution and subjob management.
Automating the organization and metadata tagging of sequencing data across projects.