HIGHLIGHTS
SUMMARY
As a consequence, the large-fruited cultivar M82 remains a primary reference for genetic, metabolic, and developmental analyses but the lack of a high-quality genome assembly causes reference bias and false signals in genomics analyses. Even after combining complementary assemblies, modern draft genome assemblies rarely achieve complete chromosome scale. Longer and ultimately chromosome-scale sequences are produced by scaffolding, the process of ordering and orienting genome assembly contigs, and placing gaps between adjacent contigs. Scaffolding is usually achieved by comparing a genome assembly to genome maps encoding the relative distances of genomic markers . . .
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