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454 data Assembly editing in GAP5 : Join contigs function

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  • 454 data Assembly editing in GAP5 : Join contigs function

    Hi,

    I am trying to reduce the number of contigs I got after an assembly run using Mira on 454 single end data. For Assembly editing, GAP5 offers an excellent function of joining contigs based on with in contig similarities. My question is, if any one have ever tried this function, how significant this joining would be based on very stringent parameter of Min overlap of 500/1000 with <15% maximum mismatch and 50-100bp, initial alignment of 100 bp. I tried to run this function with these parameteres and i got around 80 possible internal joins. But I am quite skeptical to disturb my original contigs, what if I am wrong in joining????

    Any ideas guyzz????

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