NEXTFLEX-96 DNA Barcodes

  • Compatible with NEXTFLEX® Rapid DNA-Seq 2.0, NEXTFLEX® Methyl 1 Sequencing Kit and other DNA-Seq applications
  • 8 nt index contained within adapter sequence
  • Considerably reduce your Illumina per-sample sequencing cost by multiplexing DNA-Seq samples
  • Increase your sequencing scale by pooling several samples on a single flow cell
  • Supplied in 96-well plate format or 96 microfuge tubes
  • Compatible with Illumina® next-generation sequencing platforms

  • NOVA-514105


    (in 96-well plate)
    768 rxns

  • NOVA-514106


    (in tubes)
    768 rxns
Download Manual
For research use only. Not for use in diagnostic procedures.

Pool Multiple Library Preparations in a Single Flow Cell Lane

The NEXTFLEX-96 DNA Barcodes are compatible with Illumina® sequencing and provide flexibility and high-throughput capabilities in sequencing applications. They significantly increase scale while reducing costs by allowing the user to pool multiple library preparations in a single flow cell lane. These adapters compatible with Illumina® sequencing utilize an indexed adapter with an 8 nt unique sequence. This allows for proper differentiation between samples, preventing poor reads caused by single base errors introduced during PCR. The NEXTFLEX® index is contained within the adapter sequence, eliminating the need to perform PCR to add flow cell binding sequences. The NEXTFLEX-96 DNA Barcode index sequences are designed to have a hamming distance of 4, allowing discrimination of different barcodes even in the case of an error in the barcode read.

These adapters are supplied in either a 96-well format (cat # NOVA-514105) or in microfuge tubes (cat # NOVA-514106). These barcodes can be used with single, paired-end, and multiplex reads and are compatible with the NEXTFLEX® Rapid DNA-Seq Kit 2.0, the NEXTFLEX® Methyl Sequencing Kit, the NEXTFLEX® Cell Free DNA-Seq Kit and other genomic DNA library prep protocols.

Do you want to index your samples but don’t want to use 96 different barcodes?
We also offer the NEXTFLEX® DNA Barcodes in sets of 6, 12, 24, and 48 barcodes.

Do you want to multiplex more than 96 samples?
The NEXTFLEX-HT Barcodes are ideal for researchers who want to multiplex up to 384 samples with single-index adapters.

Do you want to multiplex RNA samples?
NEXTFLEX® RNA-Seq Barcodes and NEXTFLEX-96 RNA-Seq Barcodes are also available for your RNA-Seq multiplexing needs.

Avoiding Registration Failure with Low Level Multiplexing

Registration failure could occur if the color balance was not maintained between the red and green lasers (used to sequence A/C bases and G/T bases, respectively). Read our blog post, Tech Tips – Barcode Recommendations for Low Level Multiplexing, to learn how to avoid registration failure on an Illumina® sequencer caused by lack of sufficient index sequence diversity.

DNA-Seq Multiplexing Adapter

The NEXTFLEX® adapters contain the full complement of sequencing flow cell binding regions (A, B), which eliminates the need to perform PCR to add the barcode tag.


  • NEXTFLEX-96 HT Barcode Adapter (25 µM)
  • NEXTFLEX® Primer Mix (12.5 µM)


  • Sequences of NEXTFLEX-96 DNA Barcode Indexes – Excel / PDF

Select Publications that Cite Use of the NEXTFLEX-96 DNA Barcodes: 

  • Amaroa, F., et al. (2016) Genetic characterization of Arrabida virus, a novel phlebovirus isolated in South Portugal. Virus Research. doi:10.1016/j.virusres.2016.01.004.David, L. A., et al. (2015) Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans. 6:3, doi: 10.1128/mBio.00381-15.
  • Derboven, E., Ekker, H., Kusenda, B., Bulankova, P., Riha K. (2014) Role of STN1 and DNA Polymerase α in Telomere Stability and Genome-Wide Replication in Arabidopsis. PLoS Genetics. DOI: 10.1371/journal.pgen.1004682.
  • Devall, M., et al. (2015) A comparison of mitochondrial DNA isolation methods in frozen post-mortem human brain tissue—applications for studies of mitochondrial genetics in brain disorders. Biotechniques 59(4): 241-246.
  • Henry, I. et al. (2014) Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing. Plant Cell.
  • Ivansson, E. L., et al. (2016) Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy. PNAS PLUS. doi:10.1073/pnas.1600084113.
  • Jiang, L. et al. (2014) ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells. PLoS ONE 9(4): e94187. doi: 10.1371/journal.pone.0094187.
  • Kis, O. et al. (2017) Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates. Nat. Commun. 8, 15086 doi: 10.1038/ncomms15086.
  • Kloth, M., et al. (2015) Activating ERBB2/HER2 mutations indicate susceptibility to pan-HER inhibitors in Lynch and Lynch-like colorectal cancer. Gut doi:10.1136/gutjnl-2014-309026.
  • Maheshwari, S. et al. (2015) Naturally Occurring Differences in CENH3 Affect Chromosome Segregation in Zygotic Mitosis of Hybrids. PLoS Genet. 11(1) doi:  10.1371/journal.pgen.1004970
  • Ravi, M., et. al.  (2014) A haploid genetics toolbox for Arabidopsis thaliana. Nature Communications. 5, 5334 doi: 10.1038/ncomms6334.
  • Thakur J. and Sanyal K. (Feb 2013) Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans. Genome Research. doi: 10.1101/gr.141614.112
  • Yamane A. et al. (2013) RPA Accumulation during Class Switch Recombination Represents 5′–3′ DNA-End Resection during the S–G2/M Phase of the Cell Cycle. Cell Reports.
  • Zastrow-Hayesa, G. M., et al. (2015) Southern-by-Sequencing: A Robust Screening Approach for Molecular Characterization of Genetically Modified Crops. The Plant Genome. doi:10.3835/plantgenome2014.08.0037.

The NEXTFLEX-96 DNA Barcodes Kits contain 8 reactions each of 96 unique barcodes, enabling the user to multiplex up to 96 samples. This kit is shipped on dry ice.

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