https://github.com/laura-budurlean/sv-calling-with-speedseq

A workflow for using SpeedSeq to align and call SVs from WGS data
https://github.com/laura-budurlean/sv-calling-with-speedseq

bioinformatics cnv delly freebayes lumpy speedseq structural-variation sv

Last synced: 7 months ago
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A workflow for using SpeedSeq to align and call SVs from WGS data

• Host: GitHub
• URL: https://github.com/laura-budurlean/sv-calling-with-speedseq
• Owner: laura-budurlean
• Created: 2023-04-21T19:41:18.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-08-24T06:07:23.000Z (about 1 year ago)
• Last Synced: 2025-01-27T04:35:10.098Z (9 months ago)
• Topics: bioinformatics, cnv, delly, freebayes, lumpy, speedseq, structural-variation, sv
• Language: Shell
• Homepage: https://github.com/laura-budurlean/SV-calling-with-SpeedSeq
• Size: 15.6 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# SV-calling-with-SpeedSeq

A workflow for using SpeedSeq to align and call SVs from WGS data. A simple guide to SpeedSeq to get SNV, SVs, and to generate normal, discordant, and splitter BAM files. SNV calling with Freebayes, SV calling with LUMPY DELLY is included.

See speedseq_pipeline file for details.

Additional information on SpeedSeq is available from the Hall lab at: https://github.com/hall-lab/speedseq and https://www.nature.com/articles/nmeth.3505

# SpeedSeq pipeline overview:

![speedseq](https://github.com/laura-budurlean/SV-calling-with-SpeedSeq/assets/30268603/c42cdbc2-a77c-46fb-873e-2d67a85bb485)

Image reproduced from: https://www.nature.com/articles/nmeth.3505