title: Next generation sequence assembly with AMOS.
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.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Treangen
authors.forename: Dan D
authors.initials: DD
authors.lastname: Sommer
authors.forename: Florent E
authors.initials: FE
authors.lastname: Angly
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.forename: Mihai
authors.initials: M
authors.lastname: Pop
mesh_terms: D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software