State Of The Art In Base-Calling?

Question

[asjo]

What is state-of-the art in base-calling for Sanger sequencing these days?

Does Phred+Phrap still reign supreme? Do newer or better programs exist? What are people using? Any Free (open source) implementations?

References to algorithms, implementations, or papers would be great.

[Istvan Albert]

what type of basecalling are you referring to? For high throughput sequencing the base calling has been offloaded almost entirely to the instrument and is part of the preprocessing provided by the vendor.

[asjo]

I was thinking of "classical"(?) Sanger sequencing. Sorry, I should have specified that. I have updated the question and tags accordingly.

Answer 1

[Michael Schubert]

For an alternative (and supposedly better) caller on Illumina, see this link:

Massingham, T and Goldman, N (2012) All Your Base: a fast and accurate probabilistic approach to base calling. Genome Biology 13:R13

Citations might help too.

[Gabriel R.]

I think he is referring to Sanger sequencing technology.

[Istvan Albert]

unrelated observations: the paper was submitted on July 29, 2011, accepted on Feb 29, 2012. First that's quite a long wait, then it has matching days of the months, plus a leap day - hey bioinformaticians who can tell me what's the p-value of that happening?

[Matthieu Miossec]

Not to mention that the title is an internet culture reference...

Answer 2

[Gabriel R.]

As far as I can tell yes, anyway the errors in Sanger are so low that I would not worry too much about basecalling.

[Aaronquinlan]

Except for when you are trying to call heterozygotes...spent a year and a half of my life on that...