Pristionchus Whole Genome Sequence Analysis v1

With whole genome sequencing becoming more affordable and accessible every year, more diverse research groups will be capable of overcoming barriers to entry to utilize sequencing as a powerful tool for their research. The combination of mutagenesis experiments and sequencing of genomes of model organisms provide researchers a means to study mutations responsible for observed developmental phenotypes or behaviors. Sequencing of genomes tends to produce exorbitantly large data files that require specialized tools such as Burrows-Wheeler Aligner (BWA), Samtools, and Bcftools for processing. As the amount of sequencing in labs increases, the demand for bioinformatics skill also increases. Fortunately, existing computational workflows can minimize the amount of computer-knowledge required by individuals to handle whole genome reads. Nevertheless, these workflows require individuals to manually input each command from start to finish. Depending on the size of the files or the commands used, the time required to complete individual steps can take from a few seconds to several hours; with the entire workflow potentially requiring 8 or more hours on an average laptop computer. In this protocol, we provide a method to automate a workflow designed for mapping and finding candidate suppressor mutations in the nematode Pristionchus pacificus. This protocol is a automated workflow adapted from "A simplified workflow for the analysis of whole-genome sequencing data from mutant lines with an application to the nematode Pristionchus pacificus" by Christian Rödelsperger. https://doi.org/10.1101/2020.11.12.379388