Most Accurate Algorithm:Suite To Align Sanger Sequencing Data Today

Question

[Orca]

Hi all,

Back to the "past" with Sanger sequencing data, I'm wondering what is still today the most accurate algorithm/suite to align Sanger sequencing data. Because I used Phred/Phrap/Consed 10 years ago.

Thanks for your answer.

Orc@

[Jeremy Leipzig]

the actual aligners within that stack are cross_match and swat

[Lyco]

I have been looking for an alternative to Phred/Phrap/Consed recently, something that is not quite as expensive, but did not find anything obvious. If somebody could suggest a free or cheap alternative with similar functionality, this would be great.

[Bach]

@Lyco: TraceTuner (basecalling), Lucy (sequencing vector removal), MIRA (assembly) and Staden/gap4 (finishing editor) will very probably do what you want.

Answer 1

[lh3]

The answer really depends on what speed you want. There is always a balance between accuracy, speed and memory.

Smith-Waterman, if you do not care about speed at all. Cross_match, if speed is not a big concern. SSAHA2, if you want to align many sequences against a long genome. BWA-SW, if efficiency is a big problem. GMAP/blat, if your reads are actually ESTs.

Answer 2

[Drio]

I use phred/phrap/consed on my amplicons designed to validate mutations. From what I see in the publications that's still the gold standard. I don't see any reason to change to other alternatives as the pipelines are very stable and deliver excellent results.