Documentation for BESC KB Genome Resequencing toolkit

This kit was developed for BESC genome resequencing projects. The target for resequencing is usually the genome of a strain, which is further referred to as the mutant strain, or M strain, with a practically important phenotype evolved by an adaptation of a wild type strain. This phenotype is absent in the wild type strain, or WT strain, with a completely sequenced genome, which is used as the reference genome. The goal of the resequencing projects is to discover genomic modifications underlying the specific phenotype of the mutant. The toolkit we describe here was developed to analyze sequencing data produced for the resequenced mutant genomes in terms of their biological content and in terms of physiological effects on the mutant phenotype. By developing tools we aimed not just to re-call SNPs and indels from the resequencing data, but also to facilitate the biological interpretation of the mutations by their comprehensive annotation. In addition, we sought to predict molecular functions that likely lost, gained, or changed in the mutant. Below is a brief description of tools available in the kit.