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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 indexing Dual indexing
Single end (SE) R1, R2 R1, R2, R3
Paired end (PE) R1, R2, R4 R1, R2, R3, R4

Multiplexing - dual index reads - paired end