MKDESIGNER and TASEQ: a set of tools for plant genotyping by targeted amplicon sequencing

Targeted amplicon sequencing (TAS) is a high-throughput genotyping method in which markers can be designed at desired positions. However, genotyping by TAS requires a genome-wide primer design and complex post-sequencing analyses, which are difficult for researchers who are not familiar with bioinformatics. There was a demand for an environment where researchers could easily perform data analysis for genotyping by TAS.

In this study, we developed the primer design tool MKDESIGNER and the post-sequencing analysis tool TASEQ. Using these tools, users can complete the process of primer design for TAS with just three commands, and they can also obtain the files necessary for genetic analysis with just four commands. The strategy of MKDESIGNER is that it designs as many markers as possible and then thins them out to the necessary number. This allows users to design markers that are more evenly distributed. It is also possible to reduce the density of markers around the centromere. We performed genotyping by TAS using these tools and achieved a success rate close to that reported in previous studies (approximately 80%).

MKDESIGNER and TASEQ contribute to easy implementation of genotyping by TAS in environments where next-generation sequencers are available. They are implemented in Python and are freely available in Bioconda. The source codes are available on GitHub. ( https://github.com/KChigira/mkdesigner , https://github.com/KChigira/taseq ).