PacificBlue Scaffolding Tool for PacBio Long Reads

This tool is a rudimentary implementation of a scaffolding algorithm that utilizes BLASR alignments of PacBio long reads to a genome assembly. The algorithm analyzes each PacBio read individually, stacking the alignments in an array and calculating alignment coverage along the read. This idea was inspired by Gene Myers' work on DAZZLER that he presented at the 2016 JGI Users Meeting (https://www.youtube.com/watch?v=8vg3225G8gU). The goal of analyzing the alignment coverage along each read is to find unique alignments and exclude repetitive alignments. Thus unique alignments on a read that span unassembled gaps could provide the basis for linking two sequences together (i.e. scaffolding). This project started off as a Cerulean mod (https://arxiv.org/abs/1307.7933), but quickly evolved into completely new code. However, some of the file and class names remain the same, as tribute to their origin.