TruSeq libraries were hybridized to a single-read flow cell, and individual fragments were clonally amplified by bridge amplification on board the HiSeq 2500 Rapid instrument. Once clustering was completed, the flow cell was sequenced using Illumina’s sequencing by synthesis (SBS) chemistry. Upon completion of read 1, an 8-bp index read for index 1 was performed. The index 1 product was then removed, and the template was reannealed to the flow cell surface. The run continues with seven chemistry-only cycles, followed by an 8-bp index read to read index 2.

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