The best tool to find SNPs in short amplicon sequences.

Question

[Bioin]

I am working on a amplicon sequence of length 1000 bp, my objective is to find the variations (SNPs/Indels). Can someone please suggest the best tool or method to do this.

Thank you.

[ATpoint]

Hello GP,

Your question is lacking the required details. Please start by reading this post on How To Ask Good Questions On Technical And Scientific Forums. In your case, is this a single amplicon, or is it any NGS-based experiment? Do you have sequencing data, or do you have to perform experiments first?

[Bioin]

I have few sanger sequenced PCR amplicons of length 1kb each. My objectives are 1. to find out the locus and associated genes it (each amplicon) belongs to. 2. SNPs/Indels present in each amplicon in comparison to its reference genome.

[Joe]

1. BLAST
2. Download the results from BLAST and do a multiple or pairwise sequence alignment with your sequence and however many reference sequences you want to compare. There are many, many aligners, so it will depend how many and what types of sequences you want to compare.