Next Generation Sequence Assembly with AMOS
Open Access
- 1 March 2011
- journal article
- unit
- Published by Wiley in Current Protocols in Bioinformatics
- Vol. 33 (1), 11.8.1-11.8.18
- https://doi.org/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.Curr. Protoc. Bioinform. 33:11.8.1‐11.8.18. © 2011 by John Wiley & Sons, Inc.This publication has 27 references indexed in Scilit:
- EDAR: An Efficient Error Detection and Removal Algorithm for Next Generation Sequencing DataJournal of Computational Biology, 2010
- Using the Velvet de novo Assembler for Short‐Read Sequencing TechnologiesCurrent Protocols in Bioinformatics, 2010
- A computational genomics pipeline for prokaryotic sequencing projectsBioinformatics, 2010
- Assembly of large genomes using second-generation sequencingGenome Research, 2010
- Correction of sequencing errors in a mixed set of readsBioinformatics, 2010
- Assembly algorithms for next-generation sequencing dataGenomics, 2010
- ABySS: A parallel assembler for short read sequence dataGenome Research, 2009
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphsGenome Research, 2008
- Bioinformatics challenges of new sequencing technologyTrends in Genetics, 2008
- A New Algorithm for DNA Sequence AssemblyJournal of Computational Biology, 1995