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@
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@
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.
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.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
the actual aligners within that stack are cross_match and swat
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.
@Lyco: TraceTuner (basecalling), Lucy (sequencing vector removal), MIRA (assembly) and Staden/gap4 (finishing editor) will very probably do what you want.