Comparison of sequence alignment tools

[nupurgupta]

I am dealing with aligning sequences from next-gen sources to a reference genome. I came across this great site

http://seqanswers.com/forums/showthread.php?t=43

which has a list of such tools.

Has anyone done a comparitive study of efficiency of these tools? That would be very interesting.
Thanks.

[malachig]

The authors who publish an aligner are often required to compare and contrast with existing tools. So you can reads the papers associated with aligners of interest and see if the authors convince you to use their aligner. Of course, the authors have an unavoidable bias towards their own aligner in this scenario.

A number of bloggers have discussed the question informally online. For example:

http://massgenomics.wordpress.com/2008/05/14/short-read-aligners-maq-eland-and-others/

Ideally, there would be a paper(s) written by a group that did not have their own aligner that did an objective comparison of many aligners. To be most useful, the comparison would be done with different applications in mind. These applications might have different aligner requirements (e.g. mutation discovery, expression profiling, miRNAs, ChIP-Seq, etc.).

I'm not aware of such a publication right now. Maybe someone else is and will post it. Unfortunately, journal editors (and reviewers) seem notoriously merciless towards such manuscripts ... Anything that fits into a 'platform comparison' category is automatically deemed to be less scientifically valuable, not novel, etc. Indeed some journals explicitly ban submission of this type of work.

[nupurgupta]

Thank you very much for your input.