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

SUBMITTER: Miya F 

PROVIDER: S-EPMC11844088 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature