Split seq data based on index AND barcode

[Meyana]

Dear all,

I am currently designing an experiment, where my samples will have both a barcode and an index.
Barcode: Sample-specific
Index: Reaction-specific (here: ChIP reaction)

So I might have X samples with each a unique barcode pooled together with the same index (A). And then Y samples with each a unique barcode pooled together with the same index (B).

Can anyone advice me on the best way to perform demultiplexing on this type of data?

I will specify the index on the sample sheet (here A or B), but then how to get the reads that are sample-specific, that is what I don't know how to do.

I am hoping to get help to find an established tool for this.

(sequencing will be done on MiSeq, HiSeq and/or NovaSeq)

[luc]

Could you describe where your barcodes/indices are located in the Illumina reads?
In the index reads (i5 and i7) or in-line with the forward and reverse sequence reads?

[GenoMax]

Once you separate your sample pools based on Illumina demultiplexing you can then use a tool called sabre to demultiplex individual samples from the pool.