How to troubleshoot barcode collision error when running bcl2fastq2

What is barcode collision?

An index/barcode collision error occurs when the index sequences we are using are not diverse enough to support the mismatch settings due to the edit/hamming distance being too small and there being too much similarity between them.

Barcode Collision Example 1: The two index sequences are distinct by 1 base pair. A single mismatch would result in barcode collision.

Barcode Collison example 2: The two index sequences are distinct by 2 base pair. One mismatch would also result in barcode collision.

What is hamming distance

Hamming distance measures the minimum number of substitutions required to change one sequence into the other, or the minimum number of errors that could have transformed one string into the other.

How to troubleshoot barcode collision error?

If there is barcode collision error, Add the following to the command line

--barcode-mismatch 0

Note: Barcode mismatches = # of differences allowed in the index sequence when assigning reads to samples

● Available settings: 0, 1 (default), 2

● An important distinction: This is not the number of bases different between indexes in the sample sheet

For any feedback or questions regarding this article (Illumina Knowledge Article #2326), contact Illumina Technical Support [e-mail].