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The pan-genome of a European potato
We implemented both read-mapping-based and assembly-based approaches to identified SNPs using Nipponbare as the reference genome. The pan-genome was transformed into a haplotype graph with the alignments of 40 haplotype genomes to the DM reference using minimap2. The phased SNP sites with uniquely mapped reads and mean Coverage depths greater than threefold were acquired using…
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The centuries of isolation shaped the genetics of the Greenlanders
Fatash can compute posterior probabilities of the local ancestry per genomic window per haplotype using haplotype likelihoods and genome-wide admixture proportion estimates obtained from HaploNet train and HaploNet admix. It can obtain posterior probabilities of the local ancestry per genomic window per haplotype based on haplotype likelihoods and genome-wide admixture proportion estimates obtained from HaploNet…