Next Generation Sequence Assembly with AMOS
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: Assembly of a Small Bacterial Genome
- Basic Protocol 2: Assembly of a Phage Genome
- Basic Protocol 3: Metagenomic Example Assembly
- Support Protocol 1: Downloading and Installing AMOS
- Support Protocol 2: Modifying the Minimus/Minimo Pipeline
- Support Protocol 3: Validating an Assembly Inside AMOS
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
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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. View Image -
Figure 11.8.2 Screenshot of Minimus output. View Image -
Figure 11.8.3 Screenshot of C. ruddii assembled contigs. View Image -
Figure 11.8.4 Screenshot of analyze‐read‐depth output. View Image -
Figure 11.8.5 Visualization of an assembly with Hawkeye. View Image -
Figure 11.8.6 Screenshot of Minimo usage and options. View Image -
Figure 11.8.7 Screenshot of Minimo output. View Image -
Figure 11.8.8 Screenshot of the number of contigs, average contig length, and N50 calculated by getN50. View Image -
Figure 11.8.9 Screenshot of the assembly statistics generated with getN50. View Image -
Figure 11.8.10 Screenshot of the assembly statistics generated with getN50. View Image -
Figure 11.8.11 Screenshot of goBambus2.py output. View Image -
Figure 11.8.12 Screenshot of the modules comprising the Minimus pipeline. View Image -
Figure 11.8.13 Screenshot of the number of contigs, average contig length, and N50 calculated by getN50. View Image -
Figure 11.8.14 Screenshot of amosvalidate output. View Image
Videos
Literature Cited
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| Key References | |
| Sommer et al., 2007. See above. | |
| This first publication describing Minimus focused on the algorithm and implementation details. It also includes assemblies of a gene and bacterium. | |
| Pop et al., 2004. See above. | |
| This is the original Bambus publication describing the scaffolder's algorithm and implementation. A new publication describing Bambus 2, the updated scaffolder referenced throughout this manuscript, is currently under review. | |
| Internet Resources | |
| http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS | |
| AMOS Sourceforge website, where code, tutorials and general information on AMOS can be accessed. |
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