Help: Phred quality for ab1 files
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6.0 years ago

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

sequence biojava phred chromatogram ABIF • 2.4k views
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Entering edit mode
4.8 years ago
trausch ★ 1.7k

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.

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