Command Line Program To Trim Abi Files

Question

[Greg]

Hello all,

I am looking for a free program that can read ABI trace files and allow for end trimming. I have a constantly changing set of ABI files and I want to be able to trim the ends based on the quality of the sequence. This would preferably be a command line program that I can run on Windows or Ubuntu so that I can automate it within my pipeline. I am not looking for a chromatogram view, I want something that can tell me the quality of sequence at each position.

Thank you for your help!

Answer 1

[Darked89]

pregap4 from Staden I believe should have command line interface apart from GUI.

Answer 2

[Lee Katz]

phred does this really well, but you need to contact the author to order it. Free for academic users.