[Open-bio-l] Best practices for quality trimming?

[Dan Bolser]

What is there a Standard Operating Procedure (SOP) for quality
trimming reads? i.e. which tool, what settings and for what purpose?

It seems that, when using a window, the median quality of the window
should be used as the threshold for deciding where to 'end clip'
sequences.

Is there a database of the assemblers, for example, that do or don't
take quality information into account when assembling?

I'm working on a software database for NGS tools here:

http://seqwiki.com


(It's still quite beta, and at some point it may move to http://bifx.org/wiki)


Cheers,
Dan.