What is a universal spacer sequence and how does it affect demultiplexing?

For library designs that include an identical sequence between adapter and barcode, e.g. probe-based linear barcoded adapters samples, lima offers a special mode that is activated if it finds a shared prefix sequence among all provided barcode sequences. Example:

>custombc1
ACATGACTGTGACTATCTCACACATATCAGAGTGCG
>custombc2
ACATGACTGTGACTATCTCAACACACAGACTGTGAG

In this case, lima detects the shared prefix ACATGACTGTGACTATCTCA and removes it internally from all barcodes. Subsequently, it increases the window size by the length L of the prefix sequence. If --window-size-bp N is used, the actual window size is L + N. If --window-size-mult M is used, the actual window size is (L + |bc|) * M.

Because the alignment is semi-global, a leading reference gap can be added without any penalty to the barcode score.

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