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Cosmika Goswami's pipeline for call SNPs on prokaryotic NGS data.


  • It is best to create a dedicated folder/directory in which you will carry out your work
  • Copy the snpcallphylo python executable into it and create two subfolders: input and output. You can also choose other names.
  • either copy or symlink you data files into the input directory
  • You can start to create the "configuration.ini" file first .. it needs to specify the input files. Here is a an awk commandline which will let you do that:
ls -1 `pwd`/data/*.fastq.gz | awk '{split($0,a,"/");;split(a[9],b,"_"); print b[1]"_"b[4]"="$0}'