A painless way to customize Circos plot: From data preparation to visualization using TBtools

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Abstract

<p xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" dir="auto" id="d2200549e251">Circos plots enable scientists to easily inspect big biological data genome‐widely on a macroscopic scale, but cumbersome preparation of input data and complex parameter configuration limits its application. We have developed the “Advanced Circos” function in TBtools, to provide a simple way to construct Circos plots. As an out‐of‐the‐box combo toolkit, TBtools has integrated a set of functions convenient for input data preparation. The “Advanced Circos” function is supplied with a user‐friendly interface for the customization of parameter settings and can be deployed to visualize all kinds of genomic data, such as genomic associations, alignment data, gene density, and QTL locations. In the present article, we introduce the main features of “Advance Circos” and the protocols of upstream data preparation, aiming to endow more users with the ability to use Circos plots in big genomic data exploration. </p><p xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" dir="auto" id="d2200549e256"> <div class="list"> <a class="named-anchor" id="d2200549e258">  </a> <ul> <li id="d2200549e259"> <div class="so-custom-list-content so-ol"> <p class="first" dir="auto" id="d2200549e260">An out‐of‐the‐box solution for genome‐scale data visualization</p> </div> </li> <li id="d2200549e262"> <div class="so-custom-list-content so-ol"> <p class="first" dir="auto" id="d2200549e263">A step‐by‐step protocol for Circos plot configuration</p> </div> </li> <li id="d2200549e265"> <div class="so-custom-list-content so-ol"> <p class="first" dir="auto" id="d2200549e266">Reproducible and resumable project management</p> </div> </li> </ul> </div> </p><p xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="first" dir="auto" id="d2200549e271">Coming with a handy toolkit, Advanced Circos in TBtools provides a painless way to construct Circos Plots starting from input file preparation. Tracks including associated regions, dot plots, line plots, bar plots, heatmap, feature tags, and so forth are all supported. Try it! Coordination transformation and graphics element manipulation are quite easy. <div class="boxed-text panel" id="d2200549e273"> <a class="named-anchor" id="d2200549e273">  </a> <div class="figure-container so-text-align-c"> <img alt="" class="figure" src="/document_file/ed282414-d476-47c2-814a-33d4dcba5099/PubMedCentral/image/IMT2-1-e35-g010.jpg"/> </div> <div class="panel-content"/> </div> </p>

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TBtools - an integrative toolkit developed for interactive analyses of big biological data

Chengjie Chen, Hao Chen, Yi Zhang … (2020)

The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.

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Circos: an information aesthetic for comparative genomics.

Martin Krzywinski, Jacqueline Schein, Inanç Birol … (2009)

We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Yupeng Wang, Haibao Tang, Jeremy D. DeBarry … (2012)

MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.