Base-calling, Editing and Sequence Assembly
Highly accurate base-calling is a reliable characteristic of our ABI 3130xL automated fluorescent DNA analyzer. We use the KB basecaller optimized for ABI Prism BigDye Terminator v.3.1. It provides quality scores and can provide ambiguity codes (if requested, the default is A,C,G,T,N).
We edit the base calls, for A and B mode samples. C and D mode clients must edit their own data. (Our various service levels are described on the DNA Sequencing page.) We highly recommend editing, especially truncating the low quality reads at the beginning and end of reads, prior to assembly or additional data analysis. This is especially important if you need to design primers for "primer walking" DNA sequencing.
We can perform sequence assembly using the U. Washington suite phred, phrap and consed. Please discuss your project with Dr. Keller if you anticipate needing help with assembly or subsequent data processing.