IDT for Illumina DNA/RNA Unique Dual Index Compatibility on the MiniSeq
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IDT for Illumina DNA/RNA Unique Dual Indexes are 10 bp each.
Currently the MiniSeq Reagent Cartridges are not able to complete dual 10 bp index reads without also reducing the insert read lengths to compensate for the additional index cycles.
In order to sequence the dual 10 bp indexes on the MiniSeq, set up the run with four fewer sequencing cycles, either 151+10+10+147 or 149+10+10+149.
For FASTQ Generation, Illumina recommends upgrading to MiniSeq Control Software v2.0 which has Local Run Manager 2.0
If the MiniSeq has Local Run Manager v1.3.1, add the definition files for the index kits used by adding a custom library prep kit. The definition files are available on the IDT for Illumina UD Indexes Support Page here.
For any feedback or questions regarding this article (Illumina Knowledge Article #2045), contact Illumina Technical Support .