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Introduction

Most online tutorials on genome and transcriptome assembly provide manuals on specific programs or a collection of programs integrated into an automated pipeline. That approach can get the job done quickly, but it also tends to produce sub-optimal results. We realized over time that it is far better to thoroughly understand what goes on behind the scene during the assembly process. That level of understanding has the added benefit of being able to design the sequencing experiment, because the quality of assembly varies greatly with the selected next-gen technologies and library types.

These tutorials focus on describing the conceptual steps to carry out NGS-based genome and transcriptome assemblies. Although we mention specific software programs from time to time, we encourage the readers to stay agnostic about implementations. Instead of trying to find the best end-to-end program to solve a problem, we expect you to take the view that all bioinformatics programs are ‘inherently defective’. They are defective simply because they have not been designed to work well on your combination of NGS libraries. We hope that by understanding the failure points of different programs, readers will be able to solve their problems better.