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How many index cycles can be sequenced on MiSeq?
For MiSeq Control Software (MCS) v3.1 and below, there is no limit to index cycles on MiSeq. The recommended range is 6-10 cycles. >10 cycles per index have not been tested by Illumina.
For MCS v4.0 and higher, the maximum index length is 100 cycles.
- For index lengths between 20-100 bp, use manual mode, as Local Run Manager (LRM) v3 limits index read lengths to 20 bp.