Batch trimming of Sanger reads?

[ucpete]

I've got > 100 Sanger sequences that I'd like to trim in a batch fashion based on chromatogram quality, and I don't want to do it manually. Can anyone recommend an open source solution to this problem?

Thanks!

ucpete

[sklages]

Lucy, http://lucy.sourceforge.net/

has been working in our group for years.

hth, Sven

[ucpete]

Thanks Sven. I had actually come across that page when I was searching around, but the sourceforge link is down and has been for at least a few days :/

I went ahead and filtered semi-manually but I will take a look at Lucy for future endeavors.

[sklages]

Well, currently the link is pretty alive ;-)
Lucy is fast and is doing a really good job. You might want to look at lucy2 as well.
lucy just puts the clipping offsets in the fasta header, the clipping itself has to been done externally. Lucy2 "really clips" your fasta data.

Maybe Staden's 'pregap4' is of interest as well.

cheers, Sven

[ucpete]

That's really strange Sven, when I visit http://lucy.sourceforge.net I get "The requested page is being migrated. This project/user is temporarily unavailable due to its data being migrated. Service will be restored shortly." and that has been the case for almost a week now. You're able to download from there? Anyway, I guess it doesn't really matter because I found lucy2 at http://www.complex.iastate.edu and just downloaded it. Thanks again for your help!