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Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33.

Next generation sequence assembly with AMOS.

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  • 1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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.

© 2011 by John Wiley & Sons, Inc.

PMID:
21400694
[PubMed - indexed for MEDLINE]
PMCID:
PMC3072823
Free PMC Article
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