Resources: Documentation

This protocol is for the extraction and sequencing of ultra-high molecular weight (uHMW) genomic DNA. The protocol: - Will allow the reliable generation and sequencing of ultra-long read length N50s (>50 kb) - Is optimised for high yield - Is compatible with R10.4.1 flow cells **For Research Use Only**

This protocol describes an end-to-end workflow for telomere-to-telomere sequencing of human samples. For Research Use Only This is a registration-based Early Access product.

This protocol: - Describes how to carry out barcoded Telo-Seq for native sequencing of telomeres. - Uses high molecular weight genomic DNA (HMW gDNA). - Requires custom-ordered oligos for telomere adapters and splints. - Enables accurate telomere length measurement and assigns each telomere to a chromosome arm. - Is compatible with R10.4.1 flow cells. For Research Use Only

This is a 10X Genomics Visium Spatial transcriptomics method. The protocol: - Requires cDNA amplicons produced using the Visium Spatial Gene Expression assay (Visium V1 for Fresh Frozen) or the Visium HD 3' Spatial Gene Expression assay - Has a library preparation time ~210 minutes - Has high output - Requires PCR **For Research Use Only**

This is a single-cell transcriptomics method. The protocol: - Requires cDNA amplicons produced using the 10x Genomics Chromium GEM-X Universal 3’ Gene Expression (V4) assay or the Chromium Next GEM Universal 3’ Gene Expression (V3.1) assay. - Has a library preparation time ~210 minutes - Has high output - Requires PCR For Research Use Only

This protocol: - Uses extracted RNA samples - Uses third-party reagents and primers, alongside the SQK-RBK114.96 kit - Includes reverse transcription and tiled PCR amplification - Is for multiplexing 1-96 samples - Has a library preparation time of ~315 minutes - Includes fragmentation - Is compatible with R10.4.1 flow cells **For Research Use Only**

For Research Use Only.

This is the fastest and simplest protocol to sequence plasmid DNA. The protocol: - Is for multiplexing up to 96 samples - Has a library preparation time of ~60 minutes - Has a high yield - Includes fragmentation - Is compatible with R10.4.1 flow cells For Research Use Only

This is the fastest and simplest protocol to sequence amplicon DNA. The protocol: - Is for multiplexing up to 96 single species amplicon samples - Is optimised for 500 bp to 5 kb amplicons - Has a library preparation time of ~60 minutes - Has a high yield - Includes fragmentation - Is compatible with R10.4.1 flow cells For Research Use Only

This is a rapid method to perform metagenomic sequencing for identification of bacterial, fungal and viral pathogens. The protocol: - Consists of a two-in-one method that splits into bacterial/fungal sample preparation and viral/acellular sample preparation - Provides a recommended host depletion and extraction method for respiratory samples - Uses a shotgun approach to RT-PCR - Involves tagmentation, barcoding and PCR amplification - Is compatible with R10.4.1 flow cells **For Research Use Only**

Automated rapid barcoding method using the ElysION device, outlining library preparation and sequencing. This protocol: * Is an automated method using the ElysION device * Uses genomic DNA * Enables multiplexing of up to 96 samples * Includes DNA fragmentation * Is optimised for high output * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__ This method is used with an **Early Access device**. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This protocol provides an end-to-end workflow for the analysis of pharmacogenomic (PGx) genes using adaptive sampling, and the Oxford Nanopore platform. Downstream variant calling is via the EPI2ME™ wf-pgx workflow, acquiring a minimum of 40x coverage per sample, across the PGx-associated genes. The protocol covers genomic DNA extraction, mechanical shearing, native barcoding, library preparation, sequencing, and data analysis. It supports the multiplexing of up to four samples per PromethION™ Flow Cell and is compatible with DNA extracted from human whole blood, cultured cells, or saliva. This protocol: - Uses genomic DNA extracted from human whole blood, cultured cells, or saliva - Requires DNA fragmentation - Uses the Native Barcoding Kit 24 V14 (SQK-NBD114.24) - Is compatible with R10.4.1 flow cells - Allows the analysis of data using the wf-pgx workflow in EPI2ME <br> **For Research use only**

This is a legacy method. Please refer to our new equivalent method: [SARS-CoV-2 virus PCR tiling and sequencing from RNA using SQK-RBK114.96](/document/sars-cov-2-virus-pcr-tiling-and-sequencing-from-rna-using-sqk-rbk114-96) This protocol: - Uses extracted RNA samples - Includes reverse transcription and tiled PCR amplification - Is for multiplexing 1-96 samples - Has a library preparation time of ~315 minutes - Includes fragmentation - Is compatible with R10.4.1 flow cells **For Research Use Only** __This is an Early Access product.__ For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).

This is an end-to-end method outlining sample extraction, library preparation, sequencing, and data analysis. This protocol: * Uses genomic DNA * Enables multiplexing of 4-24 samples * Takes ~60 minutes for library preparation * Includes DNA fragmentation * Is optimised for high output * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__

Automated native barcoding method using the ElysION device, outlining library preparation and sequencing. This protocol: * Enables multiplexing of up to 48 samples * Allows analysis of native DNA * Is a PCR-free method * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__ This method is used with an Early Access device. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This is a single-cell transcriptomics method. The protocol: - Requires cDNA amplicons produced using the 10x Genomics Chromium GEM-X Universal 5' Gene Expression (V3) assay or the Chromium Next GEM Universal 5' Gene Expression (V2) assay - Has a library preparation time ~140 minutes - Has high output - Requires PCR **For Research Use Only**

This document describes the steps for sample extraction, library preparation, sequencing, and data analysis. The protocol: - Uses human cfDNA - Is for singleplex sequencing - Uses the Ligation Sequencing Kit V14 (SQK-LSK114) - Is compatible with R10.4.1 flow cells <br> __For Research Use Only__

This document describes the steps for sample extraction, library preparation, sequencing, and data analysis. The protocol: - Uses human cfDNA - Enables multiplexing of 12 samples - Uses the Native Barcoding Kit 24 V14 (SQK-NBD114.24) - Is compatible with R10.4.1 flow cells <br> __For Research Use Only__

This document describes the sequencing of the influenza virus. The protocol: - Uses extracted RNA samples - Includes reverse transcription and PCR amplification using two separate primer schemes for Influenza A and Influenza B - Includes quantification and normalisation steps to ensure equal distribution of barcodes for 24, 48 and 96 samples - Is compatible with R10.4.1 flow cells <br> For Research Use Only

This is an end-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human blood samples and sheared to 30kb length - Takes ~300 minutes for sample preparation and ~90 minutes for library preparation - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This document describes the sequencing of adeno-associated viral (AAV) vectors. The protocol: * Requires the Native Barcoding Kit 24 V14 (SQK-NBD114.24) * Is PCR-free * Uses up to 24 barcodes * Allows analysis of native DNA * Is compatible with R10.4.1 flow cells For Research Use Only

This protocol: - Uses N50 of 30 kb genomic DNA extracted from human cell lines - Has sample preparation time: ~320 minutes and library preparation time: ~90 minutes - Has data analysis: 1-2 hours - Requires no PCR - Is compatible with R10.4.1 flow cells For Research Use Only

This protocol: - Uses N50 of 10 kb genomic DNA extracted from human cell lines - Has sample preparation time: ~220 minutes and library preparation time: ~90 minutes - Has data analysis time: 1-2 hours - Requires no PCR - Is compatible with R10.4.1 flow cells For Research Use Only

For Research Use Only.

This protocol: - Uses N50 of 15 kb genomic DNA extracted from human cell lines - Has sample preparation time: ~240 minutes and library preparation time: ~90 minutes - Has data analysis: 1-2 hours - Requires no PCR - Is compatible with R10.4.1 flow cells For Research Use Only

This is an end-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human blood samples and sheared to 15kb length - Takes ~240 minutes for sample preparation and ~90 minutes for library preparation - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This is an end-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human saliva samples - Takes ~300 minutes for sample preparation and ~90 minutes for library preparation. - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This is an end-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human buccal swab samples - Takes ~90 minutes for sample preparation and ~135 minutes for library preparation. - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This is an end-to-end method outlining sample extraction, library preparation, sequencing, and data analysis. The protocol: - Uses genomic DNA extracted from whole blood - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This is a rapid method to perform sequencing and analysis of *Salmonella*. The protocol: - Uses *Salmonella* colonies from overnight cultures - Includes tagmentation, barcoding, and PCR amplification - Enables multiplexing of 1-24 samples - Is compatible with R10.4.1 flow cells **For Research Use Only**

This is an end-to-end method for preparing Chromatin Accessibility libraries. This protocol: - Outlines 6mA tagging - Uses genomic DNA extracted from cell samples - Has a sample preparation time of ~340 minutes and library preparation of ~90 minutes - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This is an automated end-to-end method using the ElysION device outlining sample extraction, library preparation, sequencing, and analysis. The protocol: * Uses bacterial or fungi cells * Enables multiplexing of up to 24 samples * Includes DNA fragmentation * Is optimised for high output * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__ This method is used with an Early Access device. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This document describes an end-to-end, ultra-rapid genome sequencing protocol for blood samples. It includes preparation of genomic DNA (gDNA) from blood, sequencing and basecalling with a PromethION™ device, secondary analysis using the wf-human-variation workflow in EPI2ME™, and tertiary analysis via third party analytics platforms Fabric or Geneyx. Ultimately, this end-to-end workflow will enable you to go from sample-to-answer in ~24 hours. This protocol: - Uses gDNA extracted from human blood samples - Requires DNA fragmentation - Uses the Ligation Sequencing Kit V14 (SQK-LSK114) - Is compatible with R10.4.1 flow cells __For Research Use Only__