How to mitigate index hopping
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What is index hopping? Index hopping is a specific cause of index misassignment. Index hopping can result in incorrect assignment of libraries from the expected index to a different index in a multiplexed pool, which may lead to misalignment and inaccurate downstream analysis results.
What factors impact index hopping?
Contamination of free adapters/index primers can lead to increased index hopping.
The method of library preparation contributes to levels of index hopping. In general, PCR-free library preparation methods that only include adapter ligation generate libraries with higher levels of index hopping than methods that incorporate a subsequent PCR amplification step.
Libraries clustered on nonpatterned flow cells with traditional bridge amplification typically have lower rates of index hopping (≤ 1%) compared to libraries run on patterned flow cells that use exclusion amplification (ExAmp) cluster generation (≤ 2%).
Best practices to mitigate index hopping:
Prepare libraries with unique dual index kits, which allow index hopped reads to be bioinformatically removed.
Remove free adapters from library preps. This may include additional bead clean-up or spin column clean-up if needed.
Store libraries individually at -20°C. Do not store libraries as a pool.
Pool libraries just prior to sequencing.
More details about index hopping are found in the white paper .
For any feedback or questions regarding this article (Illumina Knowledge Article #1928), contact Illumina Technical Support .