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

Michael C. Schatz; Adam M. Phillippy; Daniel D. Sommer; Arthur L. Delcher; Daniela Puiu; Giuseppe Narzisi; Steven L. Salzberg; Mihai Pop

doi:10.1093/bib/bbr074

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

Michael C. Schatz, Adam M. Phillippy, Daniel D. Sommer, Arthur L. Delcher, Daniela Puiu, Giuseppe Narzisi, Steven L. Salzberg, Mihai Pop

School of Medicine

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

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 simplemicrobial species throughmammalian 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.

Original language	English (US)
Article number	bbr074
Pages (from-to)	213-224
Number of pages	12
Journal	Briefings in bioinformatics
Volume	14
Issue number	2
DOIs	https://doi.org/10.1093/bib/bbr074
State	Published - Mar 2013

Keywords

Assembly forensics
DNA sequencing
Genome assembly
Visual analytics

ASJC Scopus subject areas

Information Systems
Molecular Biology

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10.1093/bib/bbr074

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title = "Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies",

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 simplemicrobial species throughmammalian 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.",

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AU - Salzberg, Steven L.

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

Abstract

Keywords

ASJC Scopus subject areas

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