Help: Phred quality for ab1 files

Question

[rabidbirdman4]

Hello,

I'm using the biojava legacy release of 1.8.1 (API here: http://www.biojava.org/docs/api1.8/)

I want to get the Phred quality values for single bases in an ab1 chromatogram. Using methods in the ABITools class, I was able to create a SymbolList of the sequence.

I'm now using the PhredTools class, but I don't know where to start.

Thanks

Answer 1

[trausch]

Indigo analyses ab1 files and aligns them to a reference. The command-line version available here also dumps the chromatogram including the base-calls and the Phred quality values so this might be what you are looking for.