<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/40583?offset=240 https://bioinformaticsonline.com/bookmarks/view/28884/tgnet Wed, 24 Aug 2016 05:36:36 -0500 https://bioinformaticsonline.com/bookmarks/view/28884/tgnet <![CDATA[TGNet]]> Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. 

Visualization and quality assessment of de novo genome assemblies

Citation

This software is fully described in the paper:
Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality assessment of de novo genome assemblies.

In brief, our scripts create Cytoscape files to visualize transcript evidence that suggests adjacency between scaffolds and contigs.

Software requirements

BLAT (tested with Standalone BLAT v. 32×1). Source Binaries .
Cytoscape (tested with versions 2.7.0, 2.8.2)
a UNIX machine (tested on Mac OS X 10.6 and CentOS 4.6)

Address of the bookmark: https://github.com/ksanao/TGNet

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/31018/j-circos Fri, 17 Feb 2017 09:06:54 -0600 https://bioinformaticsonline.com/bookmarks/view/31018/j-circos <![CDATA[J-Circos]]> Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Address of the bookmark: http://www.australianprostatecentre.org/research/software/jcircos

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/41330/u-plot-genome-u-plot-sample-implementation Tue, 03 Mar 2020 01:39:12 -0600 https://bioinformaticsonline.com/bookmarks/view/41330/u-plot-genome-u-plot-sample-implementation <![CDATA[U-Plot: Genome U-Plot sample implementation]]> The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.

image

Address of the bookmark: https://github.com/gaitat/GenomeUPlot

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/44491/cgviewjs-is-a-circular-genome-viewing-tool Wed, 27 Mar 2024 11:16:24 -0500 https://bioinformaticsonline.com/bookmarks/view/44491/cgviewjs-is-a-circular-genome-viewing-tool <![CDATA[CGView.js is a Circular Genome Viewing tool]]> CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView.

CGView.js is the genome viewer of Proksee, an expert system for genome assembly, annotation and visualization.

Features

  • Circular and linear views of genomes

  • Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

  • Smooth zooming down to the sequence level

  • Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

  • Save high resolution PNG maps up to 8000x8000px

  • Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

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