Contents

01

Installation

02

Available notebooks

EPI2ME Labs extends the JupyterLab notebook framework with a pre-configured analysis environment. The notebooks contain Python code needed to run data analysis, however zero configuration of the code is required. The notebooks can be used both by students and researchers new to nanopore sequence data analysis, and more experienced bioinformaticians who are comfortable working with Python.

Installation

See the Installation page for a walkthrough to guide install the EPI2ME Labs application.

For more information on starting your tutorial journey through the EPI2ME Labs application see the Running a Tutorial section of our quick-start guide.

Available notebooks

Below you will find a complete list of available notebooks with a short description of each. Listed also are notebooks in development. The links direct to pre-rendered versions of the notebooks to provide some illustrations of the capabilities of each notebook; these pages are not interactive.

Basic Tasks

• Introduction to FASTQ - An introduction to the FASTQ format and simple file operations

• Introduction to VCF - An introduction to Variant Call Format files and their manipulation in Python and on the command line.

• Introduction to BAM - An introduction to the SAM and BAM formats for storing alignment data and their manipulation with samtools.

• Introduction to FAST5 - A guide to handling raw sequencing data from Oxford Nanopore Technologies’ sequencing devices.

• Basic QC - A simple workflow using the sequencing summary file, produced by MinKNOW and Guppy, to QC measures such as read length and quality.

• Alignment QC (Planned) - Walking through alignment of reads to a reference sequence, and and introduction to the world of samtools and pysam.

• Adaptive Sampling Inputs - A short snippet to aid the creation of the necessary files required by MinKNOW for exome Adaptive Sampling experiment.

Assembly

• Assembly tutorial - A workflow utilising Flye and Medaka to produce high quality assemblies of small to mid-sized genomes.

• Assembly assessment (Planned) - An introduction and tips on assessing the quality of an assembly using both reference-based and reference-free methods.

Metagenomics

• Post-EPI2ME 16S Analysis - A quick demonstration of adding lineage information to EPI2ME 16S output, and grouping counts by rank.
• Metagenomic assembly (Planned) - A guided approach to metagenomic assembly and assessment based on Flye’s metagenomic assembly.

cDNA and RNA

• Differential Gene Expression - Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using Nanopore long reads.

  Note: A new cDNA/RNA Nextflow workflow is planned that will include isoform detection, differential expression, fusion transcript identification and more.

Other

• EPI2ME Labs Tutorial - A meta tutorial showcasing the unique (or perhaps esoteric and idiosyncratic?) features of the EPI2ME Labs notebook environment. This is particularly useful for contributors to read.

• Clone validation - Validation of synthetic biological constructs using Nanopore sequencing rather than Sanger sequencing.

• SARS-CoV-2 Analysis - A notebook based around the ARTIC pipeline for the analysis of SARS-Cov-2 multiplexed amplicon datasets.

• Modified bases - A demonstration of the use of Medaka to process and summarise the optional modified base output of Guppy.

• Medaka tech. demo - A deep dive into the inner workings of Oxford Nanopore Technologies’ Medaka software