Hi, I have an amplicon of 1.6kb and I have sequenced it using forward and reverse primer. Now, I have to trim both the sequences and assemble those into one contiguous sequence. My goal is to align that sequence to a reference gene and its corresponding alleles. I want to see if my sequence can unambiguously distinguish different alleles or not.
Can you please suggest me suitable softwares for performing all the above mentioned steps? I know Geneious and Sequencher which need license.
Please give me some recommendation as well as some tutorials link if you have.