Why we need the Assemblathon - The Assemblathon
excerpted
If you want the best genome assembly possible, you may have to accept some trade-offs. The assemblers that may perform well in one area may not perform as well in other areas. Everybody wants to be told 'genome assembler X will give you the best assembly' but at the moment it doesn't seem fair to make such bold assertions. What we did find out from Assemblathon 1 was that a number of genome assemblers performed admirably across many, but not all, of the different metrics. For example, the assembler that did the best job at increasing coverage (the amount of the known genome present in the assembly), ranked 9th when considering the number of substitution errors present in the assembly. Conversely, the assembler that did the best job at minimizing substitution errors ranked 8th in terms of coverage. You pays your money and you takes your choice. We should mention, however, that these two assemblers (SOAPdenovo and SGA), along with ALLPATHS were consistently ranked among the best assemblers for the vast majority of metrics and were the three best overall assemblers in Assemblathon 1.
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