Exploring pan-genomics for crops

The aim was to evaluate how pan-genomics can facilitate data management and ease specific data analysis use cases in real-world crop genome collections.
PanTools was used to create pan genomes of (high quality) assemblies of a number of large, complex crop genomes: rice (5 genomes: nipponbare, 93-11, IR64, Kasakath, DJ123), tomato (3 genomes: lycopersicum, pennellii, pimpinellifolium), cucumber (2 genomes: 9930-BGI and Gy14, USDA-ARS Cucumber Improvement Program) and maize (4 genomes: B73, Mo17, PH207 and CML247).
The resources and computing time required for storing and retrieving sequences as a function of genome complexity, and verify consistency of the pan-genome with the source data was reported as well as the feasibility and potential advantages of using a pan-genome for (1) large-scale variant annotation/retrieval and (2) variation detection.

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