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Eoulsan is a command line workflow engine for Next Generation Sequencing data analysis. Eoulsan is able to execute many high throughput sequencing workflows like RNA-Seq, ChIP-Seq or scRNASeq. It could be run either in standalone mode or in distributed mode using the Hadoop framework or a more standard job scheduler.

This wiki contains all necessary information for using Eoulsan and developing plug-ins.

User documentation is available on Eoulsan website.

Basics for using Eoulsan

• Eoulsan's Concepts
• What is a design file?
• What is a workflow file?
• How to launch an analysis?

Standard analysis workflows for Eoulsan

• Analysis of bulk RNA-Seq data
• Analysis of ChIP-Seq data
• Analysis of Single cell RNA-Seq data using a SmartSeq2 protocol
• Analysis of Single cell RNA-Seq data using a 10X Genomics Chromium protocol

Using Eoulsan on a computational cluster

• Using Eoulsan with Hadoop
• Using Eoulsan with a job scheduler

Frequent asked questions

See the FAQ page.

Basics for developing with Eoulsan

See the Developer documentation.