Index hopping can occur when index sequences are incorrectly assigned to the libraries within a multiplexed pool, leading to misalignment of sequencing data. If unligated adapters are not removed after adapter ligation, they can contaminate libraries and contribute to higher index hopping rates.
The Illumina Free Adapter Blocking Reagent minimizes index hopping by blocking unligated adapters, preventing them from hybridizing and producing index-hopped strands. This enzymatic treatment can be performed on a single library or a pool of libraries after library preparation, before the denaturation step.
The Illumina Free Adapter Blocking Reagent features:
Effects of Index Misassignment on Multiplexing and Downstream Analysis
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Infinium LiHa and Infinium RoMa Operating Manual Documentation
Illumina Free Adapter Blocking Reagent Documentation
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