Which is the best best tool for quality assessment for next generation sequencing data?
If you want to analyze the quality from your fastq files from NGS sequencing, take a look to FastQC. Efficient and clear reports. You can also use it from command line in customized pipelines.
Have a look at RSeQC as well, it mainly evaluates the quality of mapping and gene coverage rather than reads quality.
I did not know this one, thank you a lot for this link Martombo.