support for paired end, variable length demultiplexing

[gregcaporaso]

Comments
This could be a new method in this plugin.

References
A user requested this support on the forum here.

[jairideout]

Came up again on the forum.

[thermokarst]

This recently came up on the forum.

[lstanish]

Any updates on this functionality? All of the recent NEON data are dual-indexed.

[thermokarst]

I think this issue can be closed, because I believe you can accomplish this using q2-cutadapt (but please correct me if I am wrong).

[lstanish]

I have the same issue as reported here, separate index files (I1 and I2) need to be merged with sequence files (R1 and R2) before demultiplexing. Looks like q2-cutadapt only works when the barcodes are already attached to the sequences?