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An overview of Illumina multiplexing

Multiplexing

  • Index 1 (i7) is always read.
  • Index 2 (i5) is read only in dual index setting.
Single indexingDual indexing
Single end (SE)R1, R2R1, R2, R3
Paired end (PE)R1, R2, R4R1, R2, R3, R4

Multiplexing - dual index reads - paired end