Snpcallphylo

Introduction

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

Procedure

• 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}'