How to assess the quality of a genome assembly without the help of a reference sequence is an open question. Only a few techniques are currently used in the literature and each has obvious bias. An additional method, restriction enzyme associated DNA (RAD) marker alignment, is proposed here. With high enough density, this method should be able to assess the quality of de novo assemblies without the biases of current methods.With the growing ambition to sequence new genomes and the accelerating ability to do so cost effectively, methods to assess the quality of reference-free genome assemblies will become increasingly important. In addition to the existing methods of EST and conserved sequence alignment, RAD marker alignment may contribute to this effort.
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