Question: Which program, tool, or strategy do you use to visualize genomic rearrangements?
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gravatar for stianlagstad
4.1 years ago by
stianlagstad970
Oslo, Norway
stianlagstad970 wrote:

Which program, tool, or strategy do you use to visualize genomic rearrangements? 

In relation to my master thesis I'm working on tools to visualize fusion genes. In that regard I'm interested in any and all strategies and tools that exists for visualizing genomic rearrangements. I'll include the list I have so far below, and update the list when I get answers.

Programming packages:

  • Circos: Perl package for circular plots, which are well suited for genomic rearrangements.
  • J-Circos is a java application for doing interactive work with circos plots.
  • ClicO FS: an interactive web-based service of Circos.
  • rCircos: R package for circular plots.
  • OmicCircos: R package for circular plots for omics data.
  • ggbio: R package for visualizing biological data. Has a circular view similar to the previous packages.
  • D3 chord diagrams (javascript) can be used to visualize genomic rearrangements. See this plot of migration flows as a similar example.
  • chimeraviz: R package for chimeric RNA/fusion gene visualizations. (Disclaimer: I wrote this package.)

"Complete" tools:

ADD COMMENTlink modified 2.6 years ago • written 4.1 years ago by stianlagstad970
3

Just as a comment somewhat related to this: To the question A: I want to know what are some of the common problems facing a Bioinformatician? my answer is: Visualization!

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by dariober10k
2

You can also use circosJS: https://github.com/nicgirault/circosJS

ADD REPLYlink written 4.1 years ago by nic.girault20

Have you used, or know of, any of those tools to visualize circular RNAs? I am thinking shashimi plot for backspliced junction reads.

ADD REPLYlink written 4.1 years ago by A. Domingues2.1k
8
gravatar for Malachi Griffith
4.1 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

I have recently been very impressed with svviz (papergit repoproject site, documentation). 

"svviz visualizes high-throughput sequencing data relevant to a structural variant. Only reads supporting the variant or the reference allele will be shown. svviz can operate in both an interactive web browser view to closely inspect individual variants, or in batch mode, allowing multiple variants (annotated in a VCF file) to be analyzed simultaneously."

 

 

svviz example visualization

 

 

ADD COMMENTlink written 4.1 years ago by Malachi Griffith17k
3
gravatar for Alex Reynolds
4.1 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

More generically, a Sankey diagram could be used for a linear, horizontal or vertical presentation of rearrangements, as opposed to the Circos-based circular approaches.

ADD COMMENTlink written 4.1 years ago by Alex Reynolds29k
2
gravatar for samuelmiver
4.1 years ago by
samuelmiver420
Centre for Genomic Regulation (Barcelona, Spain)
samuelmiver420 wrote:

One of my favourites and very easy to use:

ACT - Artemis Comparitive Tool

https://www.sanger.ac.uk/resources/software/act/

Citing the web:

ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.

ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

ADD COMMENTlink written 4.1 years ago by samuelmiver420
2
gravatar for sentausa
4.1 years ago by
sentausa640
France
sentausa640 wrote:

Yeah, why should it be circular? I used Mauve.

ADD COMMENTlink written 4.1 years ago by sentausa640
1
gravatar for Keith Callenberg
4.1 years ago by
Pittsburgh, PA
Keith Callenberg890 wrote:

A Bioconductor R package called chimera pulls in data from a large set of fusion detection tools and then can provide some visualization. Some examples can be seen on pages 8, 9 and 10 of this pdf: http://bioconductor.org/packages/release/bioc/vignettes/chimera/inst/doc/chimera.pdf

 

ADD COMMENTlink written 4.1 years ago by Keith Callenberg890
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