The whole-genome sequences of many non-model organisms have recently been determined. Using these genome sequences, next-generation sequencing based experiments such as RNA-seq and ChIP-seq have been performed and comparisons of the experiments between related species have provided new knowledge about evolution and biological processes. Although these comparisons require transformation of the genome coordinates of the reads between the species, current software tools are not suitable to convert the massive numbers of reads to the corresponding coordinates of other species’ genomes.
Izawa, A., & Sese, J. (2013). RECOT: A tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics. Source Code for Biology and Medicine, 8. https://doi.org/10.1186/1751-0473-8-6