Creating a linkage map from SNP data of a father and 100–200 sperm cells

[李允求]

Hi, 

I am currently working on the genome assembly of a insect species.
Despite its very small body size (approximately 1.5 cm), this insect has an enormous genome size (6 Gb) and is known to exhibit significant heterozygosity even within the same species. 

Previously, I created libraries from multiple individuals to obtain Hi-C data, but most of the reads were not mapped to the draft assembly derived from another individual. We tested optical genome mapping, but we yielded similar results.

Due to the difficulty of rearing and mating, we conceived the idea of creating a linkage map using sperm and the father's genotype for chromosome-scale genome assembly. We have successfully isolated more than 100 single sperm and are now moving on to the linkage analysis step.

I have no experience using linkage maps for assembly, but I am aware that stacks are commonly used for creating linkage maps. Typically, SNP information from parents and F1 or F2 generations is used for creating linkage maps. Is it possible for stacks to create a linkage map from SNP data of a father and 100–200 sperm cells?

Thanks in advance!

Best,

Jung