I am totally new with whole-genome sequencing, coding and analysis. I am now handling with huge amounts of sequencing data which I need to map reads of evolved and donor strains with the reference genome to identify recombination events, including long fragments and SNPs. I also need to differentiate between de novo mutations with SNPs transferred from donors to recipients. I need to calculate the average length of imports as well.
I had the list of mutations generated from the comparison between ref genome with donors, and ref genome with evolved strains. I can do the comparison again by using excel, but It is really handy and time-consuming. Does anyone have experience doing with this field? Any faster method to deal with this complicated analysis?