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segment-model-spy's Introduction

SegmentModel Spy

DOI

SegmentModel Spy is a an interactive visualization tool for GATK's copy-number segmentation results. In practice, it does (almost) all that PlotModeledSegments does but adds continuous panning and zooming and provides a few annotation tracks. Under the hood, SegmentModel Spy uses GenomeSpy for WebGL-based rendering. This tool is also an example of how to use GenomeSpy in a web application.

An online version is available at https://genomespy.app/segmentmodel/

Local installation (for development)

  1. git clone [email protected]:genome-spy/segment-model-spy.git
  2. cd segment-model-spy
  3. npm install
  4. npm start
  5. Browse to http://localhost:5173/ or whatever port is shown on the console.

Legal stuff and acknowledgements

Copyright (c) 2020-2024 Kari Lavikka. See LICENSE for details.

SegmentModel Spy is developed in The Systems Biology of Drug Resistance in Cancer group at the University of Helsinki.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 965193 (DECIDER) and No. 847912 (RESCUER), the Sigrid Jusélius Foundation and the Cancer Foundation Finland.

GATK is a trademark of the Broad Institute, Inc.

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segment-model-spy's Issues

Update to recent GenomeSpy version

Now this is using an ancient version, which is functional, but is not a good example of how to use @genome-spy/core as a visualization library in an application.

Error: No name has been defined for the genome assembly!

Hi

I would like to try out this tool using Arabidopsis data. However I get this error:

Error: No name has been defined for the genome assembly!

My .dict file looks like this:

@HD	VN:1.6
@SQ	SN:Chr1	LN:30427671	M5:66bcd0ba0c2303c318cfa2742cfb4203	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas
@SQ	SN:Chr2	LN:19698289	M5:837e6cf18d30dda428a08ac2cb4061f2	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas
@SQ	SN:Chr3	LN:23459830	M5:bd4bc6259143f4b4f3921367c28d07ff	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas
@SQ	SN:Chr4	LN:18585056	M5:21f56163f7e34510232448b14fce7578	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas
@SQ	SN:Chr5	LN:26975502	M5:d6cb9d0b2cf3f54e5308adaa2af79e08	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas
@SQ	SN:ChrC	LN:154478	M5:23eeba58f0f2b65fcfaeb887856c8bfb	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas
@SQ	SN:ChrM	LN:367808	M5:965cdad4966e38be06d74ef66f9317f5	UR:file:/home/gthomson/Documents/tskAmplification/GATK_CNVPipeline/TAIR10_chr_all.fas

What flag should I use to give it a name?

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