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