Hello,
I have to do a python semester project and since I wanna be a well developed bioinformatician. I decided to write one of the tools from the scratch. My aim is not discovering the wheel again, I just want to rewrite a part of the tools. However, when I look at the source code of say, platypus, cava etc.. I got overwhelmed and I felt they have already written this code why should I try it. (I am a bioengineering so coding is not my primary skill).
I just wanted to hear your advice for me? Where should I start? I am thinking of writing a indel identification( from the output of alignment) code. Is this a good point to start?
Thank you for your help
Tunc
With respect to details, I mean elaborate on what you mean by 'indel identification', for example. From a MSA or genome alignment? That will help people point you in the right direction.
We have WGS data from TGCA(https://tcga-data.nci.nih.gov/tcga/) which are aligned files. For understand what algorithm does, plus making my project, I decided to write a indel identification code.