Unit

UNIT 11.8 Next Generation Sequence Assembly with AMOS

  1. Todd J. Treangen1,
  2. Dan D. Sommer1,
  3. Florent E. Angly2,3,
  4. Sergey Koren4,
  5. Mihai Pop1,4

Published Online: 1 MAR 2011

DOI: 10.1002/0471250953.bi1108s33

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Treangen, T. J., Sommer, D. D., Angly, F. E., Koren, S. and Pop, M. 2011. Next Generation Sequence Assembly with AMOS. Current Protocols in Bioinformatics. 33:11.8:11.8.1–11.8.18.

Author Information

  1. 1

    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland

  2. 2

    Australian Centre for Ecogenomics, University of Queensland, St. Lucia, Brisbane, Australia

  3. 3

    Advanced Water Management Centre, University of Queensland, St. Lucia, Brisbane, Australia

  4. 4

    Department of Computer Science, University of Maryland, College Park, Maryland

Publication History

  1. Published Online: 1 MAR 2011
  2. Published Print: MAR 2011

Abstract

A Modular Open-Source Assembler (AMOS) was designed to offer a modular approach to genome assembly. AMOS includes a wide range of tools for assembly, including the lightweight de novo assemblers Minimus and Minimo, and Bambus 2, a robust scaffolder able to handle metagenomic and polymorphic data. This protocol describes how to configure and use AMOS for the assembly of Next Generation sequence data. Additionally, we provide three tutorial examples that include bacterial, viral, and metagenomic datasets with specific tips for improving assembly quality.Curr. Protoc. Bioinform. 33:11.8.1-11.8.18. © 2011 by John Wiley & Sons, Inc.

Keywords:

  • next-generation sequencing;
  • genome assembly;
  • open source