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Table 4 Visualization tools for assemblies

From: Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Tool and references

Description

URL

Archive Viewer [224]

Web graphical interface to make contigs and trace data changes in the National Center for Biotechnology Information (NCBI)

http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?

CBrowse [225]

SAM/BAM-based contig web browser for transcriptome assembly visualization and analysis

http://bioinfolab.muohio.edu/CBrowse/

Consed [76]

Assembly finishing package; NGS compatible

http://www.phrap.org/

ContigScape [226]

A Cytoscape plugin facilitating microbial genome gap closing

http://sourceforge.net/projects/contigscape/

DNASTAR Lasergene [227]

Analysis suite with an assembly package

http://www.dnastar.com/

EagleView [228]

An information-rich viewer for genome assemblies with data integration capability

http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/

Gap [100, 101]

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

http://staden.sourceforge.net/

Hawkeye [229]

An interactive visual analytics tool for genome assemblies. Detection of anomalies in data and visual identification and correction of assembly errors

http://amos.sourceforge.net/wiki/index.php?title=Hawkeye

Tablet [230]

A lightweight, high-performance graphical viewer for NGS assemblies and alignments

http://bioinf.scri.ac.uk/tablet