Contig_to_chr_coords takes the NCBI sequence contig file and maps contig coordinates to whole chromosome coordinates in a GTF, GFF, or BED file
Parent program: tophat
TopHat is a fast tool for splice junction mapping for RNA-Seq reads. It aligns reads to genome using the high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. It can work without a reference annotation and process mammalian-sized genomes.