We are planing to sequence 100 amplicon libraries with hiseq X10. Our library looks like the following pattern,
P7-i7-R2-gene-R1-i5-P5
We have 10 i7 index and 10 i5 index, so with the combination, there can be 100 libraries each run.
However, our sequence facility says the hiseq X10 only can recognize one index, so we can not use the index combination protocol to identify the 100 samples, is not working in our case.
Whats an alternative methods to sequence 50-100 samples at the same time if we still want to use X10? or Nextseq?