Assembly Graph Browser: interactive visualization of assembly graphs

Abstract Summary Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Brows...

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Published inBioinformatics Vol. 35; no. 18; pp. 3476 - 3478
Main Authors Mikheenko, Alla, Kolmogorov, Mikhail
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.09.2019
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Abstract Abstract Summary Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs. Availability and implementation http://www.github.com/almiheenko/AGB. Supplementary information Supplementary data are available at Bioinformatics online.
AbstractList Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs.SUMMARYCurrently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs.http://www.github.com/almiheenko/AGB.AVAILABILITY AND IMPLEMENTATIONhttp://www.github.com/almiheenko/AGB.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online.
Abstract Summary Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs. Availability and implementation http://www.github.com/almiheenko/AGB. Supplementary information Supplementary data are available at Bioinformatics online.
Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. AGB includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e., the graphs obtained by collapsing a selected set of edges), and a new approach to visualizing large assembly graphs. http://www.github.com/almiheenko/AGB. Supplementary data are available at Bioinformatics online.
Author Kolmogorov, Mikhail
Mikheenko, Alla
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