IntroMap: a signal analysis based method for the detection of genomic introgressions.

ABSTRACT:

Background

Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.

Results

We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Additionall

SUBMITTER: Shea DJ 

PROVIDER: S-EPMC5716257 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature