How to demultiplex sequences twice

I have totally 400 samples and use 4 different barcodes for every 100 samples, and then every sample has its unique barcode. So I'd like to know how to demultiplex them.

I draw a picture:

Thanks a lot!

Hi @zwbao,
Thanks for the picture! It makes your question very clear.

This is a very unusual setup, and hence will probably require a custom solution (e.g., demultiplex twice using custom scripts and then import the demultiplexed sequences to QIIME 2).

However, if your barcodes are adjacent to each other, you could just treat them as one long barcode — in which case you can probably demultiplex as usual by using this long barcode.

Where are your barcodes? Contained in the sequence reads? Header lines? a separate barcodes file?

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