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A haplotype is the genetic makeup of an individual with respect to combinations of alleles that are closely linked and tend to be inherited together. This may be one locus, several loci, or an entire chromosome.
This work introduces a wet lab and computational pipeline, Napu, for small variant calling and de novo assembly of Nanopore sequencing data, which leads to comparable performances to short-read sequencing and allows for large-scale long-read sequencing projects.
Accurate haplotypes with abundant genomic variations benefit genetic research. Here, the authors accurately construct 1,874 pig haplotypes and demonstrate their applications in genome-wide association studies, prediction of breeding values and analyses of evolutionary selection.
The authors developed an R package that enables the estimation of group size required for mouse breeding, taking into account Mendelian genetics, fertility and litter size.
