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  • #31
    Originally posted by ECO View Post
    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



    Looks relevant to the topic of this thread.
    Last edited by dan; 01-22-2009, 06:09 AM. Reason: added a note about looking for a suitable page on Wikipedia
    Homepage: Dan Bolser
    MetaBase the database of biological databases.

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    • #32
      Originally posted by regyre View Post
      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.

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      • #33
        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...

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        • #34
          This is great thank you.

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