Reading ABI chromatogram trace files with IUPAC ambiguous DNA code

Question

[chrisothal]

Using Biopython, is there any way to read ABI/SCF trace files with IUPAC ambiguous DNA codes? The R package sangerseqR has a function makeBaseCalls that sets a cutoff signal/noise ratio and sets a primary and secondary peak calls. I couldn't find out how to do this using SeqIO.

Answer 1

[Peter]

ABI files have called bases recorded in them, which is what Biopython's ABI parser (in SeqIO) gives you. It also exposes the raw data which could be used for recalling the bases with a different algorithm.

You might also consider a standalone tool like tracetuner for recalling the bases.