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Assembly strategy. B493 Sanger sequences were assembled using CAP3. Two assemblies were generated for Illumina sequences for each genotype (B493xQAL, B6274 and B7262). After left and right Velvet trimming, sequences were assembled using CAP3. A second assembly was carried out using the ABySS short read assembler. A final CAP3 assembly allowed comparison to be made among sequences from all 4 genotypes to generate a combined de novo assembly.
