I'm mainly doing (amplicon-based) resequencing over small (50-100) number of genes with the Illumina technology. Aside from the normal metrics for quality control produced by Qualimap and FastQC, I'm wondering if there's something out there (aside TEQC, see below for while) that targets specifically targetd resequencing experiments.
I'm mostly interested in assessing coverage uniformity across a number of samples sequenced for my targets. I know about TEQC but it has a number of problems, in particular related to reading in paired reads (all of my experiments are paired-end), so I'm looking at alternatives.
Is there any software for QC that can be used for these types of experiments?