Langdon, Q.K., Peris, D., Kyle, B. & Hittinger, C.T. "sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing." Molecular Biology and Evolution 35,11, 2835-2849+ (2018). [DOI: 10.1093/molbev/msy166]
sppIDer is a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication.