What are the commonly used analysis tools to compare two similar targeted sequencing runs done with Illumina?
The type of analysis I am thinking could be useful right now are:
- Amplification biases
- Basecalling biases
- Small variant calling biases
- SV calling biases
- Fusion detection biases
By targeted sequencing I mean either amplicon sequencing or pull-down enrichment sequencing protocols, which is the same to say not whole genome sequencing or whole metagenome sequencing runs.