Some scripts for parsing NGS data from: Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

• script/Mapper1.py: Mapping and calling mutations

  • Input:
    • raw sequencing reads in fastq format
      • Fasta/flu3amp.fa
  • Output: result/AllM_3

• script/Mapper2.py: Filter clones with >1 mutations and generating a table that contains amino acid information

  • Input:
    • Fasta/flu3offset
      • Fasta/BarCode
      • result/AllM_3
      • Fasta/flu3info
  • Output:
    • result/WT_N_Depth
      • result/AGenotypes
      • result/SGenotypes
      • result/SMut'

• script/Mapper3.py: Generate a table only containing mutations with high confidence in fitness estimation (high input frequency)

  • Input: result/SMut
  • Output: result/HCMut
    • tmp/sil
    • tmp/mis
    • tmp/non

AN UPDATED VERSION OF Mapper1.py AND Mapper2.py CAN BE FOUND IN REPOSITORY: https://github.com/wchnicholas/lib240