Which data formats are supported?

While it can manage any file type, it is optimized for common bioinformatics formats including FASTQ, BAM, and VCF.

What is the primary purpose of this DNAnexus skill?

It helps developers build apps, manage data objects, and run complex bioinformatics workflows on the DNAnexus cloud platform.

Does it support parallel processing of samples?

Absolutely. The skill includes specific patterns for batch processing and launching parallel subjobs for high-throughput data analysis.

Do I need the DNAnexus SDK installed to use this skill?

Yes, you should have the dxpy Python package installed and be authenticated via the command line (dx login) to execute the commands generated by this skill.

Can this skill handle Docker-based genomics apps?

Yes, it provides patterns and configuration guidance for integrating Docker containers and managing system dependencies within DNAnexus apps.

DNAnexus Genomics Integration

Name: DNAnexus Genomics Integration
Author: ricable

byricable

•

Data Science & ML

Streamlines genomics pipeline development and data management on the DNAnexus cloud platform using the dxpy Python SDK.

This skill empowers bioinformatics engineers and researchers to build, deploy, and manage scalable genomics workflows on the DNAnexus platform. It provides specialized guidance for creating cloud-native apps and applets, managing large-scale sequencing data (FASTQ, BAM, VCF), and orchestrating complex analysis pipelines via the dxpy SDK. By automating configuration tasks like dxapp.json setup and dependency management, the skill helps users focus on scientific logic while ensuring robust execution on high-performance cloud infrastructure.

Key Features

01Programmatic platform access via comprehensive dxpy SDK support

02Streamlined genomic data management for FASTQ, BAM, and VCF files

03Advanced configuration management using dxapp.json and Docker

041 GitHub stars

05Orchestration of multi-step analysis workflows and job monitoring

06Automated DNAnexus app and applet skeleton generation

Use Cases

01Building and deploying scalable bioinformatics pipelines for variant calling and alignment

02Managing large-scale sequencing data uploads and organized project storage

03Automating batch processing of multiple genomic samples across cloud resources

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent dnanexus-integration

For use in Claude.ai and ChatGPT

Download Skill