Rohu genome

Genome assembly and ddRAD analysis of Labeo rohita

Genome Assembly

ddRAD

Sample selection

Select 100 samples, removing full siblings and minimizing half siblings

#code to select sample of 100 distantly related indivdiuals from the rohu founders
vanraden <- read.table("All_grm_vanraden.dist.matrix.fun.heat.csv",
header=TRUE, sep=",")[,-1]
vanraden <- as.matrix(vanraden)
hc <- hclust(as.dist(1-vanraden), method="ward.D2")
clusters100 <- cutree(hc, k = 100, h = NULL)

set.seed(20190317)
clusters100 <- clusters100[order(sample(length(clusters100)))] #randomise order
rand100 <- clusters100[!duplicated(clusters100)] #select 100 individuals