https://github.com/kdm9/ouroborusco

Iterative extraction of busco loci from short read datasets for phylo purposes
https://github.com/kdm9/ouroborusco

Last synced: 2 months ago
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Iterative extraction of busco loci from short read datasets for phylo purposes

• Host: GitHub
• URL: https://github.com/kdm9/ouroborusco
• Owner: kdm9
• Created: 2020-01-30T08:15:51.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2021-01-19T11:34:33.000Z (over 4 years ago)
• Last Synced: 2025-02-14T18:52:47.220Z (4 months ago)
• Language: Python
• Size: 6.84 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# ouroborUSCO

Iterative extraction of busco loci from short read datasets for phylo purposes

essentially just:

```

for iter in 1..N do

  align reads to $ref

  call variants w/ mpileup

  update $ref with $variants

  extract target regions from $ref, set to new $ref 

```

Hopefully after ~5-10 iterations this converges on each sample's true genotype