Browse documentation & protocols

Chemistry Technical Document

Data Analysis Technical Document

PCR tiling of SARS-CoV-2 virus - rapid barcoding (SQK-RBK110.96)

Rapid Sequencing Kit V14 - gDNA (SQK-RAD114)

Ligation sequencing DNA V14 - dual barcoding (SQK-NBD114.24 with EXP-PBC096)

Flow Cell Wash Kit (EXP-WSH004 or EXP-WSH004-XL)

Direct RNA sequencing - sequence-specific (SQK-RNA002)

Rapid sequencing gDNA - whole genome amplification (SQK-RAD004)

Rapid sequencing gDNA - Field Sequencing Kit (SQK-LRK001)

Rapid sequencing gDNA - barcoding (SQK-RBK110.96)

Ligation sequencing influenza whole genome (SQK-LSK109 with EXP-NBD196)

Ultra-Long DNA Sequencing Kit V14 (SQK-ULK114)

Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24)

Library recovery from flow cells

Ligation sequencing V14 - PCR barcoding (SQK-LSK114 with EXP-PBC001 or EXP-PBC096)

Rapid sequencing V14 - Plasmid sequencing (SQK-RBK114.24 or SQK-RBK114.96)

Nanopore-only Microbial Isolate Sequencing Solution (NO-MISS) - automated ElysION (SQK-RBK114.96)

Ligation sequencing gDNA - Cas9 enrichment (SQK-CS9109)

Ligation sequencing amplicons - native barcoding (SQK-LSK109 with EXP-NBD104 and EXP-NBD114)

Rapid sequencing DNA - PCR Barcoding (SQK-RPB004)

Rapid sequencing plasmids (SQK-RBK004)

cDNA-PCR Sequencing (SQK-PCS111)

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 - Rapid Barcoding Kit 96 V14 and Midnight RT PCR Expansion (SQK-RBK114.96 and EXP-MRT001)

Direct RNA sequencing (SQK-RNA002)

Workflow: Pore-C [wf-pore-c]

Human saliva DNA

Data Releases: Updated Tumor Normal Pair Benchmark Dataset

Human blood RNA

Rapid sequencing DNA V14 - barcoding (SQK-RBK114.24 or SQK-RBK114.96)

Plant leaf RNA

Ligation sequencing amplicons - Native Barcoding Kit 96 V14 (SQK-NBD114.96)

Gram-negative bacterial DNA

Yeast DNA

Direct RNA sequencing - control experiment (SQK-RNA002)

Drosophila DNA

Rapid Sequencing Kit V14 - Lambda control (SQK-RAD114)

Soil DNA

Articles: Transition from EPI2ME Agent to EPI2ME Desktop

Xenopus tropicalis DNA

Yeast DNA

MinION Mk 1B IT requirements

How Tos: Simulating sequencing datasets

Ligation sequencing gDNA - Cas9 enrichment (SQK-LSK109)

Articles: London Calling 2024

Globin mRNA depletion

FFPE cell line DNA

Tuberculosis DNA

C. elegans RNA

Articles: The first EPI2ME Hackathon

How Tos: Comparing sequences with dot plots

PCR tiling of SARS-CoV-2 virus - classic protocol (SQK-LSK109 with EXP-NBD196)

Ligation sequencing amplicons - PCR barcoding (SQK-LSK109 with EXP-PBC001)

Ligation sequencing gDNA - exome enrichment (SQK-LSK109)

Ligation sequencing DNA XL V14 (SQK-LSK114-XL)

C. elegans DNA

Ligation sequencing amplicons V14 (SQK-LSK114)

Rapid sequencing DNA - Viral metagenomics for respiratory samples and skin lesion swabs (SQK-RPB004)

Ligation sequencing V14 - Direct cDNA sequencing (SQK-LSK114)

Ligation sequencing gDNA V14 - Lambda control (SQK-LSK114)

Ligation sequencing gDNA - Native Barcoding Kit 24 V14 (SQK-NBD114.24)

Articles: Coding everything, everywhere, all at once

Data Releases: Sequencing A Tumor Normal Pair with Ligation Sequencing Kit V14

Agarose plug

Ligation sequencing gDNA - low input by PCR (SQK-LSK109 with EXP-PCA001)

Workflow: Transcriptomes [wf-transcriptomes]

Ligation sequencing gDNA - PCR barcoding (SQK-LSK109 with EXP-PBC001)

Ligation sequencing gDNA - sequence capture (SQK-LSK109)

Ligation sequencing amplicons (SQK-LSK109)

Software Releases: Online tool "Bed Bugs" for validating input files for adaptive sampling experiments with MinKNOW

Ligation sequencing gDNA - whole genome amplification (SQK-LSK109)

EPI2ME Workflows

Automated high molecular weight gDNA extraction from blood

Drosophila RNA

EPI2ME Desktop Installation

Ligation sequencing amplicons - dual barcoding (SQK-LSK109 with EXP-NBD104, EXP-NBD114, and EXP-PBC096)

Ligation sequencing gDNA - PCR barcoding (SQK-LSK109 with EXP-PBC096)

MinION Mk1C Technical Specification

Ligation sequencing amplicons - PCR barcoding (SQK-LSK109 with EXP-PBC096)

PCR tiling of SARS-CoV-2 virus - automated Hamilton NGS STAR 96 (SQK-LSK109 with EXP-NBD196)

Data Releases: Genome in a Bottle Ashkenazi Trio with Ligation Sequencing Kit V14

Data Releases: Sequencing Genome in a Bottle samples

Influenza RNA

Software Releases: EPI2ME 24.03-01 Release

Workflow: 16s [wf-16s]

Articles: Input directory structure for EPI2ME workflows

Articles: Supporting Future Clinical Bioinformaticians

SPRI size selection protocol for >1.5-2 kb DNA fragments

High output, long read sequencing from human blood

Ligation sequencing gDNA - sequence capture (SQK-LSK110)

Flongle Adapter Technical Specification

Ligation sequencing gDNA - native barcoding (SQK-LSK109 with EXP-NBD196)

Single-cell transcriptomics with cDNA prepared using 10X Genomics

Ligation sequencing gDNA - Native Barcoding Kit 96 V14 (SQK-NBD114.96)

Rapid sequencing gDNA - Lambda control (SQK-RAD004)

Ligation sequencing gDNA - exome enrichment (SQK-LSK110)

Ligation sequencing gDNA - Lambda control (SQK-LSK109)

Articles: A guide to reviewing BAM files

How Tos: How to align your data

How Tos: Unexpected results, so now what?

Ligation sequencing gDNA - whole genome amplification (SQK-LSK110)

Ligation sequencing amplicons - PCR barcoding (SQK-LSK110 with EXP-PBC001)

Rapid Sequencing gDNA (SQK-RAD004)

PCR tiling of African Swine Fever (ASF) virus (SQK-LSK109 with EXP-NBD104 or EXP-NBD114)

EPI2ME Troubleshooting Guide

Ligation sequencing gDNA (SQK-LSK110)

Ligation sequencing gDNA - Lambda control (SQK-LSK110)

Ligation sequencing amplicons - custom PCR UMI (SQK-LSK109)

Ligation sequencing amplicons - native barcoding (SQK-LSK109 with EXP-NBD196)

Workflow: Clone validation [wf-clone-validation]

Rapid sequencing gDNA - barcoding (SQK-RBK004)

Flow Cell Check

Articles: Querying a VCF file

MinION Mk1D IT requirements

Ligation sequencing gDNA - PCR barcoding (SQK-LSK110 with EXP-PBC096)

Ligation sequencing amplicons - PCR barcoding (SQK-LSK110 with EXP-PBC096)

Ligation sequencing gDNA - low input by PCR (SQK-LSK110 with EXP-PCA001)

Ligation sequencing amplicons (SQK-LSK110)

MinION Mk1B user manual

Rapid sequencing amplicons - 16S barcoding (SQK-16S024)

Ligation sequencing gDNA - native barcoding (SQK-LSK109 with EXP-NBD104 and EXP-NBD114)

Human cell line RNA

Ligation sequencing gDNA (SQK-LSK109)

Whole genomic colony PCR

Ligation sequencing gDNA - PCR barcoding (SQK-LSK110 with EXP-PBC001)

MinION Mk1C user manual

Articles: IGV for EPI2ME workflows

PCR-cDNA Barcoding Kit (SQK-PCB111.24)

EPI2ME Oxford Nanopore Open Data Project

How Tos: Singularity for Bioinformatics

MinION Mk1D Technical Specification

How Tos: How to interpret exit codes

EPI2ME Frequently Asked Questions

MinION Mk1C IT Requirements

Ligation sequencing DNA V14 (SQK-LSK114)

Ligation sequencing V14 - low input by PCR (SQK-LSK114 with EXP-PCA001)

Ligation sequencing gDNA V14 — whole genome amplification (SQK-LSK114)

Articles: Benchmarking performance with sensitivity, specificity, precision and recall

How Tos: How to build and use databases to run wf-metagenomics and wf-16s offline

Data Releases: Modified Base Best Practices and Benchmarking

PromethION 2 Integrated IT requirements

EPI2ME Quick Start

How Tos: Creating correlation plots from bedMethyl files

PromethION 2 Integrated Technical Specification

Workflow: AAV vector quality control [wf-aav-qc]

Software Releases:EPI2ME 24.08-01 Release

Workflow: Alignment [wf-alignment]

Workflow: Mycobacterium Tuberculosis Antimicrobial Resistance Identification [wf-tb-amr]

How Tos: Targeted BRCA Gene Analysis with Oxford Nanopore

Data Releases: Community contributions to Oxford Nanopore Open Data project

Safety and regulatory information

Ligation sequencing gDNA V14 - Adeno-associated virus sequencing (SQK-NBD114.24)

Data Releases: Nanopore-only T2T assembly of a human genome

How Tos: An update on our Copy Number Analysis workflow

PCR tiling of SARS-CoV-2 virus - Eco protocol (SQK-LSK109 with EXP-NBD104, EXP-NBD114 or EXP-NBD196)

Rapid sequencing V14 - Amplicon sequencing (SQK-RBK114.24 or SQK-RBK114.96)

Workflow: Amplicon [wf-amplicon]

How Tos: Short Tandem Repeat expansion genotyping in wf-human-variation

EPI2ME Downloads and resources

Workflow: Artic SARS-CoV-2 Analysis [wf-artic]

Workflow: Bacterial assembly and annotation [wf-bacterial-genomes]

Nanopore-only Microbial Isolate Sequencing Solution (NO-MISS) - Rapid Barcoding Kit V14 (SQK-RBK114.24 or SQK-RBK114.96)

Articles: The road not taken

Articles: Nextflow and Jupyter Labs

Rapid sequencing DNA - 16S Barcoding Kit 24 V14 (SQK-16S114.24)

Workflow: Basecalling [wf-basecalling]

Workflow: Influenza Typing [wf-flu]

Workflow: Single cell [wf-single-cell]

Mushroom DNA

How Tos: Selecting the correct databases in the wf-metagenomics

How Tos: Influenza Workflow

Workflow: Cas9 enrichment [wf-cas9]

Workflow: Human variation [wf-human-variation]

Workflow: Metagenomics [wf-metagenomics]

Articles: SARS-CoV-2 Midnight Chemistry V14 Update

Workflow: Mpox metagenomics assembly [wf-mpx]

Workflow: Somatic variation [wf-somatic-variation]

How Tos: Mpox Workflow

Data Releases: An experimental extremely high-accuracy, ultra-long sequencing kit