Synthetic Biology PacBio/JAWS QC Analysis (PBJ) v3.0
This software was designed as a sequence validation tool for the assembly of synthetic constructs. It analyzes FASTQ files against a list of reference sequences, combining the results from eight sequencing libraries to generate a summary, and the files needed to view the results in the Integrative Genomics Viewer (IGV) application for manual verification. This was developed for FASTQ files generated by PacBio sequencing, but could be used on any FASTQ files that do not have paired end reads. It can be used to analyze one - eight libraries at a time, and assumes that each construct sequence in the reference will be in each pool, however, this is not a requirement. This is used to identify which libraries of pooled sequences contains a perfect match, or fixable match to the reference file. This pipeline uses many freely available open source libraries, the value added is that in our application the steps of the pipeline are defined in Workflow Description Language (WDL) and run through the Cromwell workflow engine in Docker containers, for easy distribution and set up, as well as the user friendly html summary that is generated.