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https://github.com/aguilar-gomez/pumilioanalysis

Analysis of Bocas del Toro exome sequecing Oophaga pumilio samples

https://github.com/aguilar-gomez/pumilioanalysis

Science Score: 26.0%

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Analysis of Bocas del Toro exome sequecing Oophaga pumilio samples

Basic Info
  • Host: GitHub
  • Owner: aguilar-gomez
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.75 MB
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  • Watchers: 2
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Created over 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

pumilioAnalysis

Publication and preprint associated

Evolution and Diversification of the Aposematic Poison Frog, Oophaga pumilio, in Bocas del Toro Diana Aguilar-Gómez, Layla Freeborn, Lin Yuan, Lydia L. Smith, Alex Guzman, Andrew H. Vaughn, Emma Steigerwald, Adam Stuckert, Yusan Yang, Tyler Linderoth, Matthew MacManes, Corinne Richards-Zawacki, Rasmus Nielsen bioRxiv 2024.08.02.606438; doi: https://doi.org/10.1101/2024.08.02.606438

Analysis of Bocas del Toro exome sequecing Oophaga pumilio samples

1 Process reads:

  • Trimmomatic:
    • Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
    • Remove leading low quality or N bases (below quality 3) (LEADING:3)
    • Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
    • Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
    • Drop reads below the 75 bases long (MINLEN:75)
  • Prinseq:
    • Remove low complexity reads
    • Remove overrepresented reads
  • Fastqc
    • Asses quality of reads

2 Mapping:

  • Bwa mem
  • Samtools:
    • Samfile flags to exclude:
    • read unmapped (0x4), mate unmapped (0x8), not primary alignment (0x100), read fails platform/vendor quality checks (0x200), read is PCR or optical duplicate (0x400) = 1804

## 3 Filtering: - Angsd: - Minimum individuals with 1x: 250, Maximum depth per individual: 50x - minMapQ: 25, minQ: 25 - SNPpval: 1e-6 (this was removed when we wanted to process all sites including non-variant) - skipTriallelic, Removebads, uniqueOnly, onlyProper pairs

  • snpCleaner
    • Excess of heterozygous pval: 1e-6
    • Base quality bias pval: 1e-100
    • Strand bias pval: 1e-4
    • End distance bias pval: 1e-4
    • Map quality bias pval: 1e-4

## 4 Population structure: - PCAngsd

5 Color genomics

  • gemma
  • selscan
  • PBS and FST scans

6 Selection test

  • HKA test
  • Tajima`s D
  • Pi

7 Demographic History

  • dadi
  • Treemix
  • Admixed Bayes
  • 4-pop test

Owner

  • Login: aguilar-gomez
  • Kind: user

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