Most of these algorithms could not handle markers from all the chromosomes for our NGS data [ 9]. 3) REDHORSE compares hybrids against only the parental lines to determine the break points.
In addition, REDHORSE detected 59 positions where double crossovers between closely positioned markers, including some that occurred in multiple progeny (Additional file 1: Table S2); the nature and significance of these are discussed further below.
These MSAs are then used as inputs to existing RD algorithms [ 2- 5] 2) The RD algorithm in REDHORSE uses markers throughout the genome to find crossovers.
Bunt et al. (Bunt et al., 2013) found that juvenile Black Redhorse exploit groundwater seepages as thermal refuges and improved water quality.
REDHORSE detected a total of 79 distinct conventional crossovers among the 24 progeny based on these markers.
The break points separated by less than 5 kb (recombinants 5 7) were detected by the DC detection algorithm in REDHORSE.
REDHORSE was initially used to compare the ME49 and VAND reference genomes thereby identifying 499,470 informative SNPs that differ between the parental clones and for which there was sufficient data to genotype >70% of the progeny.
The break points separated by greater than 5 kb (recombinants 1 4) were all detected by the CC detection algorithm in REDHORSE.
A representative chromosome VIII from the two parental strains (ME49 and VAND) of Toxoplasma gondii and three hybrids (see section Datasets) from a recently described genetic cross [ 9] were used to demonstrate the utility of REDHORSE on NGS datasets.
