Herein I list 4 tools most used small RNA-Seq:

1) Based on Encode 

https://www.encodeproject.org/pipelines/ENCPL337CSA/

2) iSmaRT

http://bioinformatics.oxfordjournals.org/content/early/2017/01/05/bioinformatics.btw734.abstract

3) iMir

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-362

4) miRDeep2

https://www.mdc-berlin.de/8551903/en/

Hope this helps you!

Please visit these pages:

http://sfg.stanford.edu/quality.html

https://wikis.utexas.edu/display/bioiteam/Evaluating+your+raw+sequencing+data

Thank you for such interesting question and useful answers, sorry I do not have an answer but I really found it very intriguing. 

Although I am late but I think if I share my book chapter, it could be helpful.

https://link.springer.com/chapter/10.1007/978-94-024-1045-7_10