BED-Craft for nanopore adaptive sampling: a tool for generating bed files with gene names as input data for enrichment sequencing.

Abstract

Objective: Adaptive sampling, a nanopore sequencing method that enriches regions of interest (ROI), is cost-effective and useful. However, the process of defining targeted regions and creating the corresponding definition file (.bed file) are time-consuming and laborious. To simplify this process, we have developed a tool to easily create a .bed file for adaptive sampling directly from gene names.

Results: The tool is freely available on GitHub at https://github.com/medicalbioinfo/BED-Craft . The input is a text file containing one or more gene names (symbols), and even with a large number of input genes (e.g., thousands), the resulting .bed file is generated in less than a second. The length of the buffer region added upstream and downstream of the ROI is designed to account for genome strand orientation, ensuring efficient adaptive sampling. The buffer length can also be modified by the user. The tool supports the genomes of human hg19, hg38, T2T-CHM13, and other species. For researchers unfamiliar with command-line input, a GUI version of the tool is also available at https://keio-cmg.jp/BED-Craft/ . This easy-to-use .bed file generation tool enables adaptive sampling by easily changing the target genes of interest in nanopore sequencing, and provide great benefits to researchers and diagnostic laboratories.