{"repo":"PacificBiosciences/SVTopo","free":true,"listed":false,"github":"https://github.com/PacificBiosciences/SVTopo","clone":"git clone https://github.com/PacificBiosciences/SVTopo.git","description":"Complex structural variant visualization for HiFi sequencing data","language":"Rust","stars":51,"topics":["bioinformatics","data-visualization","genomics","genomics-visualization","hifi","structural-variants","structural-variation"],"license":null,"category":"analytics","readme_excerpt":"SVTopo Complex structural variant visualization for HiFi sequencing data SVTopo represents complex structural variants (SVs) to enhance PacBio HiFi data analysis. SVTopo determines connections between SV breakends using VCF and aligned BAM inputs, performing best when paired with the sawfish variant caller. SVTopo outputs connected breakends as JSON data and uses the SVTopoVz python utility to plot complex structural rearrangements as high-quality images. Key Features (see Result Interpretation for more details): Top section: illustration of connected aligned sequences as blocks, showing order and orientation in the sample genome relative to the reference Alignment support strength shown by block weight Block sizes encoded into legend Optional gene annotations Bottom section: chained plot highlighting deletion, duplication, and inversion effects on rearranged genome structure Example SVTopo image from HG002 rearrangement Getting started See the Getting started section in the User Guide to start using SVTopo See also Result interpretation for examples and explanation of SVTopo images Support information SVTopo is a pre-release software intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that SVTopo lives up to the quality that PacBio strives for, we make no warranty regarding this software. As SVTopo is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists","default_branch":null,"files":null,"tree":[],"storefront":"/r/PacificBiosciences","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/PacificBiosciences/SVTopo/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}