Which orientation are the indexes in Top_Unknown_Barcodes output from BclConvert?

For The NextSeq 1000/2000 and NovaSeq X/X Plus platforms, the RunInfo.xml file includes the IsReverseComplement flag. With this flag, the index sequences that BCL Convert recognizes and outputs are in the following orientations in the Top_Unknown_Barcodes output file.

• Index 1: the i7 index column is in the forward orientation (match the orientation if the i7 indexes in the sample sheet).

• Index 2: the i5 index column is in the reverse complement orientation (are the reverse complement of the i5 indexes in the sample sheet).

Note: For the MiSeq i100, the i7 will be in the forward orientation, while the i5 can be in the forward orientation (if doing Index First workflow) or in the reverse complement orientation (if doing Read First workflow).

For all instruments, the indexes shown in the Top_Unknown_Barcodes are in the same orientation as they are sequenced/read by the sequencer.

• See Guidelines for reverse complementing i5 sequences for demultiplexing for more information.

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