De-Bruijn Graph Constructor Package for De-novo Genome Assembly

De-novo sequence assembly is the process of constructing a contiguous long sequence out of shorter sub-sequences produced by sequencing platforms, without referring to a reference genome. It is an essential task in many biological studies today, including population and medical studies. The initial stages of de-novo assembly require the construction of a de-bruijn graph (DBG) from sequencing reads, the compression of a de-bruijn graph into a unitig graph, and the compression of multiple unitigs and nodes into contigs, supported by evidence from mapping paired-end reads. A coherent ecosystem of computational tools and packages allow researchers to quickly implement and test their ideas. For bioinformatics, Julia already offers such an ecosystem in the form of the BioJulia & EcoJulia projects, and additional independent packages. This project will add sequence assembly tools to the BioJulia ecosystem, specifically: 1) DBG construction from reads, 2) UG construction from a DBG and 3) Constructing contigs using unitigs. These tools will allow researchers to quickly construct and analyze the contigs obtained from a set of reads.