Is there a universal sequencing read preprocessing tool

Question

[murali]

Is there any universal tool which preprocess the reads of (especially human genome) any sequencing technology?

For example, I come across Prinseq tool which performs the trimming and filtering, etc.

[Devon Ryan]

I don't think you'll find a perfect magic wand. There are just too many use cases. A better question might be, "What is your preprocessing tool of choice and for what situations do you use it"? If there isn't a forum post on this (I haven't searched extensively) then perhaps there should be :)

Answer 1

[Istvan Albert]

There is no such thing as universal preprocessing because the range of problems that can occur before, during and after sequencing is very large. In addition the magnitude of data also strongly influences the choice of tools. For example prinseq is a neat tool but it has been written in perl and thus may be (many) orders of magnitude times slower on some operations than other tools. That may immediately exclude it from some considerations.