<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38224?offset=460 https://bioinformaticsonline.com/bookmarks/view/44571/panacus-a-counting-tool-for-pangenome-graphs Fri, 14 Jun 2024 14:42:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44571/panacus-a-counting-tool-for-pangenome-graphs <![CDATA[Panacus : A Counting Tool for Pangenome Graphs]]> panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

  • coverage histogram
  • pangenome growth statistics
  • path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

]]> Neel https://bioinformaticsonline.com/bookmarks/view/40594/gfaviz-flexible-and-interactive-visualization-of-gfa-sequence-graphs Thu, 23 Jan 2020 07:33:46 -0600 https://bioinformaticsonline.com/bookmarks/view/40594/gfaviz-flexible-and-interactive-visualization-of-gfa-sequence-graphs <![CDATA[GfaViz: flexible and interactive visualization of GFA sequence graphs]]> GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequence graphs, including scaffolding graphs, alignment graphs, variant graphs and splicing graphs.

Address of the bookmark: https://github.com/ggonnella/gfaviz

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