I'm Mark, the author of EULER-SR a short read assembler.
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Hi Mark,
I'm sitting in Dr. Pevzner's talk at CHI and he's talking about EULER-SR...he had to skip the algorithmic discussion in the interests of time...but we'd love to hear about it in it's own thread...
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prolly have to register to download code ... looks like "frontier" research
rudy
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A short description of EULER-SR
Originally posted by apfejes View PostThanks for introducing yourself - care to post a link and a description to your assembler?
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
If you're coming from an academic or research institution, you can download it from:
The publication above is mainly regarding 454 reads, which I spent a lot of time getting it to work well on. Since then I've optimized it for Illumina reads as well, which mainly involved modifications that reduced memory usage - an E. coli assembly with 80X coverage runs on my desktop.
If you want to assemble Illumina reads, go ahead and download the software. The code that is pending publication is for the special case when you've run the sequencer dry of reagents, producing 50-60nt reads that have low quality ends.
For the next few days I've taken downloads offline since I need to improve the interface to euler-sr so that it is a bit more easy to run.Last edited by mchaisso; 06-17-2008, 12:54 PM.
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Originally posted by ECO View PostHi Mark,
I'm sitting in Dr. Pevzner's talk at CHI and he's talking about EULER-SR...he had to skip the algorithmic discussion in the interests of time...but we'd love to hear about it in it's own thread...
I'll present a poster about this at ISMB next month... let me know if you want to hear about it now.
-mark
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Originally posted by mchaisso View PostIf you want to assemble Illumina reads, go ahead and download the software. The code that is pending publication is for the special case when you've run the sequencer dry of reagents, producing 50-60nt reads that have low quality ends.
For the next few days I've taken downloads offline since I need to improve the interface to euler-sr so that it is a bit more easy to run.
Cheers,
Scott.
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