BED-Craft

BED-Craft generates BED files from gene names to facilitate nanopore adaptive sequencing enrichment of regions of interest.

Key Features:

• Gene-to-BED conversion: Accepts a text file containing one or more gene symbols as input and generates a .bed file in less than a second, even with thousands of input genes.
• Strand-aware buffer regions: Adds upstream and downstream buffer regions around regions of interest that account for genome strand orientation to ensure efficient adaptive sampling.
• Customizable buffer length: Allows users to modify the length of the buffer regions added to the regions of interest.
• Multiple genome support: Supports human genomes hg19, hg38, T2T-CHM13, and genomes of other species.

Scientific Applications:

• Nanopore adaptive sampling: Enables enrichment sequencing by generating target definition files that allow researchers to easily change target genes of interest in nanopore sequencing experiments.
• Research and diagnostic sequencing: Provides benefits to researchers and diagnostic laboratories performing targeted nanopore sequencing by streamlining the creation of region definition files.

Methodology:

The tool converts gene symbols to genomic coordinates and outputs a .bed file with user-modifiable buffer regions added upstream and downstream of the regions of interest, accounting for genome strand orientation.