The best short read aligner

[Deutsche]

Hello! I haven't found a compatible forum for this thread and I have desided to write here.

Scientists, could you tell me please which short read aligner is the fastest?
I thought that it is Bowtie recenty but now I have some doubts about it.
Please, help me.

[zee]

I think any of the BWT aligners would be the fastest if you did a fair benchmark.

[Deutsche]

Thank you. Could You tell me what is the basis of your answer? Is it your experience or some knowledge or something else?

[n00c]

BWT-based mappers are theoretically fastest ones up until certain read length (don't remember exactly, but something like 400-1000 bp). There is a bunch of papers out there describing this.

Bowtie is extremely fast but it is arguable whether it is the best one since the definition of "best" depends on your application. For example, Bowtie is one of the best ones for RNA-seq, but no so much for resequencing, targeted sequencing, and whole-genome sequencing, where many people prefer BWA.

[nilshomer]

BWT-based mappers are theoretically fastest ones up until certain read length (don't remember exactly, but something like 400-1000 bp). There is a bunch of papers out there describing this.
.

In theory no, in practice yes. Short read mappers are heuristics, where as something like BWT-SW is not.