Bacillus thuringiensis (Bt) which is a spore-forming gram-positive bacterium, has been used as the most successful microbial pesticide for decades. Its toxin genes (cry) have been successfully used for the development of GM crops against pests. We have previously developed a web-based insecticidal gene mining tool BtToxin\_scanner, which has been proved to be the most important method for mining cry genes from Bt genome sequences. To facilitate efficiently mining major toxin genes and novel virulence factors from large-scale Bt genomic data, we re-design this tool with a new workflow. Here we present BtToxin\_Digger, a comprehensive, high-throughput and easy-to-use Bt toxin mining tool. It runs fast and can get rich, accurate and useful results for downstream analysis and experiment designs. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the addition of other query sequences. Availability and Implementation: The BtToxin\_Digger codes and instructions are freely available at https://github.com/BMBGenomics/BtToxin\_Digger. A web server of BtToxin\_Digger can be found at http://bcam.hzau.edu.cn/BtToxin\_Digger. ### Competing Interest Statement The authors have declared no competing interest.
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