Please contact your Illumina representative if you have questions about instrument specific use cases. In general, the sample sheet use cases for each instrument are listed below.

NovaSeq:
Version 1 chemistry: ALWAYS forward i7 and forward i5 indexes
Version 1.5 chemistry: ALWAYS forward i7 and reverse i5 indexes
 
NextSeq500/550/1000/2000:
 
NextSeq500/550 is on software version 4.0 or greater, which one to use is dependent on how you set up the run:
*	Local Run Manager run mode with FASTQ generation: ALWAYS forward (i7 and i5 indexes). Local Run Manager (LRM) will automatically reverse complement the i5 sequence to the correct orientation in the final sample sheet. So, the template needs to keep the i5 sequence in the forward orientation. Use the sample sheet labeled: "..._i5_Forward.csv"
*	Manual run mode with bcl2fastq or FASTQ generation in BaseSpace: i7 in forward and i5 in REVERSE COMPLEMENT orientation. The sample sheet attached in manual mode will pass directly to FASTQ generation software without further processing. Use the sample sheet labeled: "..._i5_Reverse.csv"
 
NextSeq500/550 is on the older version of software:
*	Manual mode with bcl2fastq or FASTQ generation in BaseSpace is the only option: The sample sheet must have the i5 in the REVERSE COMPLEMENT orientation. Use the sample sheet labeled: "..._i5_Reverse.csv"
 
NextSeq1000/2000:
*	For Cloud, Hybrid, and Standalone run modes, v2 sample sheets are required and generated through the "Instrument Run Tab" in Basespace. Please contact an Illumina representative for training on v2 sample sheet generation, but you can use the HT UDI sequences provided in any other template to fill in those required fields.
*	For Standalone LOCAL run mode: The sample sheet attached in manual mode will pass directly to FASTQ generation software without further processing. Use the sample sheet labeled: "..._i5_Reverse.csv"
