I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each.
Here is a rough workflow for generating the reads:
- Expression of a library of sequence variants for a heterogeneous protein of interest in phage.
- Selection of high-fitness variants according to a custom assay.
- Extraction of the variant pool via amplification of the variable region of the gene of interest.
- Preparation of Illumina sequencing library from the amplicon pool.
- Deep sequencing of the amplicon pool.
I've already combined the paired-end reads with USearch and manually removed sequences with subpar quality scores, but I now need to translate all of the remaining DNA sequences into amino acid sequences. I'm uncertain of where to begin addressing this issue, and I was hoping someone could point me in the direction of an application or python package that could assist me.
My goal: Count the abundances of each sequence variant within the Illumina data to identify which of the protein sequences are the most fit.