Here is my problem. After get a draft genome (viral) through de novo assembly, I am looking for the mutations. In particular I am looking for variants respect to a specific viral reference genome (let s call it X), which can be different than the one assembled.
Here is my current approach:
- Get DRAFT GENOME from de novo assembly;
- Align DRAFT GENOME and specific reference X with MAFFT;
- Now I have DRAFT GENOME and reference X with same coordinates;
- Maps reads on the DRAFT GENOME;
- Variant Call on the obtained bam, using X as bcftools reference.
Am I overthinking?