i5 Index Orientation Table

This table describes how to enter the i5 sequence, Forward (F) or Reverse Complement (RC), depending on the instrument and software used.

  • LRM: Local Run Manager

  • IEM: Illumina Experiment Manager

  • BSSH: BaseSpace Sequence Hub

  • IRM: Illumina Run Manager

  • Manual Edit: When manually preparing the Sample Sheet in the text editor

Instrument

i5 Index Orientation Used Based on Run Setup Tool

Standalone bcl2fastq or BSSH FASTQ Generation

Standalone BCL Convert

MiSeq

F (LRM, IEM)

F

F

F (LRM, Preptab, IEM)

RC

RC

iSeq 100

F (LRM, IEM)

RC

RC

NextSeq 500/550

F (LRM, Preptab, IEM)

RC

RC

NextSeq 1000/2000

F (Manual Edit, BSSH Run Planning)

RC

F

NovaSeq 6000 (v1.5 kits)

RC (Manual Edit), F (BSSH Run Planning)

RC

RC

NovaSeq X/X Plus

F (IRM, BSSH Run Planning)

RC

F

MiSeq i100 Series

F (IRM, BSSH Run Planning)

F (index-first) RC (read-first)

F

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