Guideline to order indexing primers / adapters via IDT

Please use IDT’s Custom Adapter Configurator tool to select the appropriate Oligos or adapters. Currently the DcGC uses 8bp unique dual indexes so we highly recommend to order also 8bp to allow you samples being mixed with other samples to fill complete FCs. Otherwise we will load your sample on complete FCs or if possible on separate FC lanes.

Here a short guided tour with the IDT guide through the oligo selection process for a TruSeq library preparation design. If you are aiming at a tagmentation based library preparation (Nextera) change the first selection under “1. Select the library prep method” to ‘Nextera compatible’, the rest of the dialog will be comparable.

1. Select the library preparation method

1. Select the Unique dual indexing option since the NovaSeq Sequencer from Illumina uses clustered flowcells

3. Select the specific type of adapter or indexing Primer

Option A: provides you index including adapters for ligation based library preparation

Option B: provides you stubby universal adapter that are used for the initial ligation followed by the also provided index containing PCR primers

Option C: provides you only the TruSeq specific Indexing PCR primers

4. Select the index length, currently 8bp’s:

5. Select the specific indices / adapters

For ease of use we internally have named the 384 8bp indizes / adapters from IDT :

  • Set A: indices #1 – 96
  • Set B: indices #97 – 192
  • Set C: indiced #193 – 288
  • Set D: indices #289 – 348

Set A and D are currently used by us, so please select indices from Set C (1st priority) or Set B (2nd priority, since partially used by us).

Order oligos from alternative providers:

In case you want to order your oligo’s from another provider feel free, for your help here the specific oligo information for the different lib prep methods. IMPORTANT: please get informed about the correct sense / antisense direction when taking the index sequences from the IDT provided excel sheets. This is tricky and prep method dependent for particularly the i7 index.

TruSeq Indexing Primers

TruSeq i7 Primer

5' CAAGCAGAAGACGGCATACGAGAT [i5] GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T

TruSeq i5 Primer

5' AATGATACGGCGACCACCGAGATCTACAC [i7] ACACTCTTTCCCTACACGACGCTCTTCCGATC*T

Nextera Indexing Primers

Index 1 Read

5' CAAGCAGAAGACGGCATACGAGAT [i7] GTCTCGTGGGCTCG*G

Index 2 Read

5' AATGATACGGCGACCACCGAGATCTACAC [i5] TCGTCGGCAGCGT*C