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Assembly visualization software tools | De novo genome sequencing data analysis

One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short subsequences produced by current technologies. The final stages of the genome assembly process inevitably require manual inspection of…
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Staden Package
Desktop

Staden Package

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and…

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). The package also covers most of the standard sequence analysis tasks such as restriction site…

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Tablet
Desktop

Tablet

A lightweight, high-performance graphical viewer for next-generation sequence…

A lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations…

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ABySS-Explorer
Desktop

ABySS-Explorer

An interactive Java application that employs a novel graph-based representation…

An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in…

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Consed
Desktop

Consed

A program for viewing and editing assemblies prepared by the Phrap assembly…

A program for viewing and editing assemblies prepared by the Phrap assembly program. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer,…

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EagleView
Desktop

EagleView

An information-rich viewer for next-generation genome assembles with data…

An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine…

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Icarus
Web
Desktop

Icarus

A novel genome visualizer for accurate assessment and analysis of genomic draft…

A novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is…

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Bandage
Desktop

Bandage Bioinformatics Application for Navigating De novo Assembly Graphs Easily

A tool for visualising assembly graphs with connections. Users can zoom in to…

A tool for visualising assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colours and extracting…

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DNPTrapper
Desktop
Web

DNPTrapper

An assembly editing and visualization tool specifically designed for manual…

An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. DNPTrapper differs from previous tools by providing flexibility and an overview…

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TGNet
Desktop

TGNet Transcript to Genome Consistency Network

Generates tables for visualization in Cytoscape from FASTA sequence and…

Generates tables for visualization in Cytoscape from FASTA sequence and scaffolding information files. TGNet contains scripts that evaluates genome scaffolding by aligning independently obtained…

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Gap
Desktop

Gap

A sequence assembly viewer and editor. The contig editor displays sequences…

A sequence assembly viewer and editor. The contig editor displays sequences along with their per-base quality values as gray scales. Discrepancies between the sequence and the consensus may be…

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SMRT View
Desktop

SMRT View

An open source Genome Browser that visualizes data generated by PacBio®…

An open source Genome Browser that visualizes data generated by PacBio® Sequencing Systems. You can explore and interact with all types of analysis results, including resequencing, de novo, cDNA,…

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Assembly…
Web

Assembly Archive Viewer

A graphical interface to contig and trace data in NCBI’s Assembly Archive.…

A graphical interface to contig and trace data in NCBI’s Assembly Archive. The assembly archive was designed to accept two types of data: assembly instructions describing the location and sequence…

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