BED-Craft is a tool that allows you to easily generate BED files, which are required for nanopore adaptive sampling, using multiple gene names as input files.
Details of this tool have been described in a paper by Miya F and Kosaki K, BMC Res. Notes, 18, 79 (2025). If you submit a paper using this tool, please cite the paper.

Input Data (Gene symbols)

Select or drag a .txt file with one gene name per line. Or paste the list into the text area below.

add_notes Drag & Drop .txt file here or use the file selector above.

The list within the selected file. You can also add and delete gene names in this section.

Options

Genome

You can choose the version of the human reference genomes from either hg19, hg38, and CHM13, mouse reference genomes mm10 and mm39. Command line version of this tool support for over 200 species. If you wish to target genomes other than those shown above, please visit the GitHub site.

Buffer Size

bp
You can set the length of the extended region ("buffer") that is set on both sides of the genes. The default size is 50000.

Chr add

You can choose whether or not to add "chr" to the chromosome number. The default is yes.