Ensemblex pipeline overview

The Ensemblex pipeline was developed to facilitate the application of each of Ensemblex's constituent demultiplexing tools and seamlessly integrate the output files into the Ensemblex framework. We provide two distinct, yet highly comparable pipelines:

1. Demultiplexing with prior genotype information
2. Demultiplexing without prior genotype information

The pipelines comprise of four distinct steps:

1. Selection of Ensemblex pipeline and establishing the working directory (Set up)
2. Prepare input files for constituent genetic demultiplexing tools
3. Genetic demultiplexing by constituent demultiplexing tools
4. Application of the Ensemblex framework

Each step of the pipeline is comprehensively described in the following sections of the Ensemblex documentation.

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