Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies

Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L., Pop, M. (March 2013) Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics, 14 (2). pp. 213-224. ISSN 14675463

URL: http://www.ncbi.nlm.nih.gov/pubmed/22199379
DOI: 10.1093/bib/bbr074

Abstract

Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Schatz lab
CSHL Cancer Center Program > Cancer Genetics
Depositing User: Matt Covey
Date: March 2013
Date Deposited: 23 May 2013 14:52
Last Modified: 14 Oct 2015 20:38
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28335

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