<![CDATA[BOL: Circleator]]> https://bioinformaticsonline.com/bookmarks/view/33693/circleator? https://bioinformaticsonline.com/bookmarks/view/33693/circleator Sun, 25 Jun 2017 18:04:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33693/circleator <![CDATA[Circleator]]> The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Sample Circleator image

Common uses of the tool include:

  • Displaying the sequence and/or genes in a GenBank flat file.
  • Highlighting differences and/or similarities in gene content between related organisms.
  • Comparing SNPs and indels between closely-related strains or serovars.
  • Comparing gene expression values across multiple samples or timepoints.
  • Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

  • Builds on BioPerl and the input file formats that it supports, including:
  • Accepts a number of other commonly-used datatypes and file formats:
    • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
  • Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
  • Requires only a single configuration file whose layout mirrors that of the figure itself.
    • Predefined configuration files and "track" types are supplied for common datasets.
    • Advanced features allow limited analyses to be performed as a figure is drawn.
  • Includes an extensive set of regression tests.
  • Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

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