FastQC is good for visualizing reads for a single sample, and MultiQC can be used to combine output from individual FastQCs into a single, clear visualization. A little HTML/CSS knowledge here will help.
The qc should include sample demultiplexing, adapter trimming, and denoising. Then FastQC and MultiQC can be used to visualize how samples change before and after each step. So you could have a pre-trim FastQC, post-trim FastQC, pre-denoise FastQC, post-denoise FastQC, etc. Then MultiQC can be used to visualize everything.
These guys have a really good example of what I mean.
FastQC is good for visualizing reads for a single sample, and MultiQC can be used to combine output from individual FastQCs into a single, clear visualization. A little HTML/CSS knowledge here will help.
The qc should include sample demultiplexing, adapter trimming, and denoising. Then FastQC and MultiQC can be used to visualize how samples change before and after each step. So you could have a pre-trim FastQC, post-trim FastQC, pre-denoise FastQC, post-denoise FastQC, etc. Then MultiQC can be used to visualize everything.
These guys have a really good example of what I mean.