NCM 2023: Singapore and Houston
  17th - 19th May
Native Barcoding Expansion 96

A versatile method of preparing a high number of barcoded sequencing libraries for applications where high throughput is required. We recommend using our latest version: Native Barcoding Kit 96 V14 (SQK-NBD114.96).

Note: This is only compatible with Kit 9 chemistry.

This product is scheduled to be discontinued. The recommended replacement is SQK-NBD114.96.

  • These Products are nearing their end of life and will soon be discontinued
  • Users need to contact customer support to discuss project completion timelines
  • Warranty periods of 3 months or more
  • Product discontinuation within 3-6 months
  • Lead time visible in store
  • Product subject to availability


This kit is recommended for users who:

  • wish to multiplex a high number of samples to reduce price per sample
  • need a PCR-free method of multiplexing to preserve additional information such as base modifications
  • require control over read length
  • are interested in utlising upstream processes such as size selection or whole genome amplifcation
  • want to optimise their sequencing experiement or throughput

Please note that to use this kit, you will need to purchase additional 3rd party reagents: see the "3rd Party Materials" tab for more detail.

Please note: This is only compatible with Kit 9 chemistry.

This product is soon to be discontinued.
This kit is soon to be discontinued and we recommend all customers to upgrade to the latest chemistry for their relevant kit which is available on the Store. If customers require further support for any ongoing critical experiments using a Legacy product, please contact Customer Support via email:

Barcoding or multiplexing is useful when the amount of data required per sample is less than the total amount of data that can be generated from a single flow cell: it allows a user to pool multiple samples and sequence them together, making more efficient use of the flow cell.

Multiplexing samples onto one flow cell can reduce the cost per sample for a user. Below are some worked examples:

No barcodes6 barcodes12 barcodes96 barcodes
Flow cell price$500$500$500$500
Library price$99$99$99$99
Barcode price-$25$50$100
Price per sample$599$104$54$7.3

The Native Barcoding Expansion is an expansion pack providing 96 unique barcodes, to enable PCR-free multiplexing of dsDNA samples such as:

  • gDNA - use in combination with Ligation Sequencing kit
  • cDNA - use in combination with Direct cDNA Sequencing kit

The Native Barcoding Kit features:

Preparation time80 minutes
Input requirement400 ng gDNA per sample, 200 fmol (130 kb for 1 kb amplicons) DNA per sample
PCR RequiredNo
Read lengthEqual to fragement length
Kit chemistryKit 9
Associated protocolsLigation sequencing gDNA - native barcoding (SQK-LSK109 with EXP-NBD196)
Ligation sequencing amplicons - native barcoding (SQK-LSK109 with EXP-NBD196)
PCR tiling of SARS-CoV-2 virus - classic protocol (SQK-LSK109 with EXP-NBD104, EXP-NBD114 or EXP-NBD196)
PCR tiling of SARS-CoV-2 virus - Eco protocol (SQK-LSK109 with EXP-NBD104, EXP-NBD114 or EXP-NBD196)
PCR tiling of SARS-CoV-2 virus - automated Hamilton NGS STAR 96 (SQK-LSK109 with EXP-NBD196)
Pack size12 reactions
StabilityShipped at 2–8°C

Long-term storage -20°C

Oxford Nanopore Technologies deem the useful life of the product to be 3 months from receipt by the customer.

The library preparation method is similar to the Ligation Sequencing Kit protocol; DNA ends are repaired and dA-tailed using the NEBNext End Repair/dA-tailing module, and then a unique dT-tailed barcode adapter is ligated on the dA-tailed template. Barcoded samples are then pooled together. Each barcode adapter also has a cohesive end and this is used as a hook to ligate to the supplied sequencing adapters.

The kit is optimised to generate maximum throughput, without the need for PCR. For highest data yields, we recommend starting with a total of 200 fmol of pure input DNA (for two samples, this means starting with 100 fmol of each). Starting with lower amounts of input material, or impure samples can affect library preparation efficiency and lower sequencing throughput.

In order to ensure that 200 fmol of total DNA is used, it is possible to generate the required number of molecules by shearing samples using a Covaris g-TUBE: 1 μg of gDNA sheared to ~8 kb corresponds to 200 fmol. However, if your experiment requires long reads, fragmentation/shearing is neither advised nor required. Note, if long reads are required, then long fragments must be present in the starting material. To determine purity, we suggest using the Nanodrop to measure the A260/280 and A260/230 ratios and we recommend that the sample should meet the following criteria:

  • A260/280 = 1.8
  • A260/230 = 2.0-2.2

The Native Barcoding Expansion is compatible with upstream processes such as whole genome amplification (for applications where under 1 ng of sample is available) and size selection (for enrichment of specified fragment lengths, using the BluePippin, for example). When size selecting, we recommend increasing the amount of input used, as size selection can be a wasteful process.

Deconvolution of barcoded sequencing data is supported by Guppy and MinKNOW, which classify the barcode sequence and sort reads into corresponding folders.

Further considerations:

Starting with lower amounts of input material, or impure samples can affect library preparation efficiency and lower sequencing throughput. PCR can be used to generate more input material in cases where sample amount is limiting. Also, where sample purity is compromised and library preparation efficiency may be reduced, PCR will select for molecules which have been successfully adapted, and generate more of them. The original impurity is lost or diluted. It is often observed that a sample which produces poor sequencing results can be improved by inclusion of PCR (for example, using the PCR Barcoding Kit).

Shipping and logistics:

Flow cells and kits are shipped together in an environmentally friendly temperature-controlled shipping box.

Products are shipped to customers within the USA and EU Monday to Thursday. Shipments to Canada, Norway, Korea and Japan are expedited Monday to Wednesday; with Australia and New Zealand leaving our warehouses on a Friday. Shipments to the rest of the world are made on Mondays to allow the full working week for packages to arrive.

The delivery charges are calculated when a quote is raised or during checkout. Once an order is made, the delivery ID and delivery information can be tracked in the Store.


Native barcoding workflow

Data analysis

Data from a Native Barcoding experiment can be analysed using:

  • the Guppy basecalling software
  • Barcode demultiplexing in the MinKNOW software

What's in the box

The Native Barcoding Expansion 96 contains 96 unique barcodes and sufficient reagents for 12 sequencing libraries.

2021-09-14 Native Barcoding 96 kit contents v2 columns

NameAcronymCap colourNo. of vialsFill volume per vial (μl)
Native Barcode 01-96NB01-96-1 plate40 μl per well
Adapter Mix IIAMIIGreen170

3rd party materials

  • NEB Blunt/TA Ligase Master Mix (M0367)
  • NEBNext® Quick Ligation Reaction Buffer (NEB B6058)
  • NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (cat # E7180S)

Alternatively to the NEBNext® Companion Module and the NEBNext® Quick Ligation Reaction Buffer, you can use the three NEBNext® products below:

  • NEBNext FFPE Repair Mix (M6630)
  • NEBNext Ultra II End repair/dA-tailing Module (E7546)
  • NEBNext Quick Ligation Module (E6056)
  • Agencourt AMPure XP beads
  • Eppendorf twin.tec® PCR plate 96 LoBind, semi-skirted (Cat # 0030129504) with heat seals
  • 1.5 ml Eppendorf DNA LoBind tubes
  • 0.2 ml thin-walled PCR tubes
  • Nuclease-free water (e.g. ThermoFisher, cat # AM9937)
  • Freshly prepared 70% ethanol in nuclease-free water


The Native Barcoding Expansion 96 can be used together with:


Flow cells

  • FLO-MIN106D


  • MinION Mk1B
  • MinION Mk1C
  • GridION