Pseudoseq

Fake genomes, fake sequencing, real insights.

Description

The Pseudoseq package allows you to build arbitrary genomes, and simulate DNA sequencing experiments. DNA sequencing experiments are modelled conceptually as a sampling process.

Install

Pseudoseq is built with BioJulia, and is designed with compatibility with the BioJulia ecosystem of tools in mind. Pseudoseq is made available to install through BioJulia's package registry.

Julia by default only watches the "General" package registry, so before you start, you should add the BioJulia package registry.

Start a julia terminal, hit the ] key to enter pkg mode (you should see the prompt change from julia> to pkg> ), then enter the following command:

registry add https://github.com/BioJulia/BioJuliaRegistry.git

After you've added the registry, you can install Pseudoseq from the julia REPL. Press ] to enter pkg mode again, and enter the following:

add Pseudoseq

Testing

Pseudoseq is tested against Julia 1.X on Linux, OS X, and Windows.