SppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing.

ABSTRACT: The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, 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. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with

SUBMITTER: Langdon QK 

PROVIDER: S-EPMC6231485 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature