Next generation sequence assembly with AMOS

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Databases, Genetic
  • Genomics / methods*
  • Sequence Analysis, DNA / methods*
  • Software*