I’d like to announce a package I’ve been working on for my research group here at the Earlham Institute, (the first full julia project… I think I’m getting to them ) that is currently close to release. There are some features left to implement, but it is usable now.
It is called Pseudoseq, and it is a package designed for the simulation of DNA sequencing experiments.
The idea is not to replicate in sillico any specific machine or technology that exists, but instead to represent sequencing in the abstract, as a sampling process. This allows us to gain insight into the assumptions and intricacies of genome assembly algorithms, and test our abstract understanding vs reality. Currently I’m working on the ability to create abitrary chromosomes/genomes with certain features relevant to the genome assembly problem.