Beginner's Handbook of Next Generation Sequencing

Everything you need to know about starting a sequencing project

Massively parallel sequencing or next generation sequencing is becoming a ubiquitous technology in basic biology research and starting to make inroads in both diagnostic and clinical settings. Despite its popularity, understanding how it works usually requires reading several manuscripts, translating technology jargon and stitching together tidbits from presentations or discussions with colleagues. This handbook is designed to assist those new to next generation sequencing get from nucleic acid sample to next generation sequencing data on the first try. Avoiding sequencing redo’s saves a lot of time and research money!

Section I, Designing a Sequencing Run outlines what you should consider when you first decide you’d like to sequence your sample. Section II, Library Preparation goes into choosing a library prep kit, considerations for calculating the coverage you need for DNA or RNA applications and determining whether targeted or global whole genome sequencing makes more sense for your application. Section III, briefly summarizes considerations for how your DNA or RNA should be fragmented and best practices for isolation and shipping your sample to a NGS services provider. Section IV, Recommendations for Analyzing your Sequencing Data, highlights types of biotinformatics services and the providers available to perform analysis of your raw sequencing data.

This is a living handbook, meaning we actively update it to keep current with fast changing technology. If you’d like to add something, please send us a message at

I. Designing a Sequencing Run

Instrument-Specific Considerations:

II. Library Preparation

Library prep considerations for:

III. Preparing your Sample for Library Preparation

IV. Recommendations for Analyzing Your Sequencing Data