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. 2011 Mar:Chapter 11:Unit 11.8.
doi: 10.1002/0471250953.bi1108s33.

Next generation sequence assembly with AMOS

Todd J Treangen  1 , Dan D Sommer, Florent E Angly, Sergey Koren, Mihai Pop
Affiliations

Next generation sequence assembly with AMOS

Todd J Treangen et al. Curr Protoc Bioinformatics. 2011 Mar.

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.

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Figures

Figure 11.8.1
Figure 11.8.1
Overview of the AMOS assembly pipeline. On the left-hand side we see the various AMOS assembly pipelines and modules, including: Minimus/Minimo, and Bambus 2.0/goBambus2. On the right-hand side we see the interaction between each individual module and the AMOS bank, a database that stores the reads, overlaps, layouts, contigs, contig links, contig edges, repeats, scaffolds and assembly information.
Figure 11.8.2
Figure 11.8.2
Screenshot of Minimus output
Figure 11.8.3
Figure 11.8.3
Screenshot of C. ruddii assembled contigs
Figure 11.8.4
Figure 11.8.4
Screenshot of analyze-read-depth output
Figure 11.8.5
Figure 11.8.5
Visualization of an assembly with Hawkeye.
Figure 11.8.6
Figure 11.8.6
Screenshot of Minimo usage and options.
Figure 11.8.7
Figure 11.8.7
Screenshot of Minimo output.
Figure 11.8.8
Figure 11.8.8
Screenshot of the number of contigs, average contig length and N50 calculated by getN50.
Figure 11.8.9
Figure 11.8.9
Screenshot of the assembly statistics generated with getN50.
Figure 11.8.10
Figure 11.8.10
Screenshot of the assembly statistics generated with getN50.
Figure 11.8.11
Figure 11.8.11
Screenshot of goBambus2.py output.
Figure 11.8.12
Figure 11.8.12
Screenshot of the modules comprising the minimus pipeline
Figure 11.8.13
Figure 11.8.13
Screenshot of the number of contigs, average contig length and N50 calculated by getN50.
Figure 11.8.14
Figure 11.8.14
Screenshot of amosvalidate output
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