[dan]

I'm definitely out of my league in this discussion, but if anyone needs hosting for some of these sample datasets, let me know!

Can we make a wiki to store all the datasets and results? A nice table would be soo cool! Also, I think people contributing data and analysis to a wiki page is more 'cite-able' than forum posts, although this is clearly an effective mechanism for community discussion. A wiki page to summarize this thread could be a good 'citation'. I tried to find a suitable spot on Wikipedia, but they don't even have an article for next-generation sequencing yet, never mind short read aligners to cope with the data.

I'd like to start benchmarking the de-novo aligners (where accuracy is much harder to pin down). This will become more and more of an issue as all the genome sequencing projects move over to next-gen technology.


BTW, anyone seen this:

I’ll be attending the coveted Marco Island meeting early next month (February 4-8), where I’ll present a poster on my evaluations of short read aligners for next-gen sequencing data

http://www.massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html

Looks relevant to the topic of this thread.

[der_eiskern]

Hi lh3,

Thanks for the original benchmarking! I'm actually looking for such a benchmarking including the latest tools, like ZOOM!, bowtie, R Biostings pairwiseAlignment(), etc. Has anybody heard of that?

Cheers,

N.

I second this. I'd be interested in a comparison of erroneous mappings with the dominant WGS alignment-to-ref tools.

[joa_ds]

Hi there, i am under some pressure to deliver results from a solexa run. They did a run, and all i had to do was give them a list of variants.

Problem is, i ran bowtie, give them the list. They verify with Sanger sequencing, and the results are different. So i used MAQ then. Results different than BowTie results (but also different than the 'reality' obtained with Sanger).

So I have a lot of questionmarks... If results vary depending on the mapping software, well, my neighboor's genome has not changed since i pressed the MAQ button, so that is a problem.

You guys still think using Eland will give me some 'strength' in explaining i did the best possible mapping i could do?

Problem is that they have multiple genotypes mixed and are looking for QTL's, so a 40% or 60% variant, in the 'normal world' is just a heterozygous variant, in QTL world, it is a big difference...

[Nomijill]

This is great thank you.