Calculating linkage disequilibrium (LD) from Pool-seq data

[2019-12-06]

Pool sequencing data does not contain individual genotype data and hence the linear combinations of alleles per genotype cannot be known. In other words haplotype information is lost.
What we know are allele frequencies per pool
We have linear allele combination information per read which is limited by the sequencing technology used, i.e. for the hugely popular and currently state-of-the-art short-read fluorescence-based sequencing technology by Illumina, this is limited to 150bp tp 300bp, and an impressive ~2Mbp using nanopore sequencing.
Considering short-read sequencing, should we look for overlapping sequences (which can be very rare if they exist at all) to somehow piece-together a longer sequence. This approach will not work for deliberately sparse genome coverage approches such as genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RADseq).
Tests using LDx which does computes LD per sequencing read and therefore severely limited by maximum read length; shows that wthin this short range of 0-300 bp, the decay of LD is not yet evident (see scatterplots below).