I am wondering why some Illumina platform (e.g. HiSeq) allow for sequencing of libraries with no index reads, while others do not (e.g. NovaSeq and MiSeq)? Are index reads used for cluster identification in the latter case?
The simple reason is aim/purpose of sequencing experiment. The the meaning of indesx itself.
If there is no need to separate different samples, there is no need of index.
Thank you for your answer. I am asking because I have in-line barcodes in my Illumina libraries that are sequenced by an external company on HiSeq. Due to discontinuation of HiSeq, the company urged me to include standard indexes in the design but I cannot quite understand why in-line barcodes would not be compatible with other sequencing platforms, like NovaSeq.
Maybe you can find answer to your question here
https://www.seqanswers.com/forum/sequencing-technologies-companies/illumina-solexa/65455-novaseq-experience
And apart from the seque3ncing itself, there are other issues as well why it need to be used a different set of barcodes for NovaSeq
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