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Open Access Highly Accessed Methodology article

Normalized N50 assembly metric using gap-restricted co-linear chaining

Veli Mäkinen*, Leena Salmela and Johannes Ylinen

Author affiliations

Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, P.O. Box 68 (Gustaf Hällstromin katu 2b), Helsinki, 00014, Finland

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Citation and License

BMC Bioinformatics 2012, 13:255  doi:10.1186/1471-2105-13-255

Published: 3 October 2012



For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-order concatenation of scaffolds (contigs). Especially for scaffold assemblies it is non-trivial to combine a correctness measure to the N50 values, and the current methods for doing this are rather involved.


We propose a simple but rigorous normalized N50 assembly metric that combines N50 with such a correctness measure; assembly is split into as many parts as necessary to align each part to the reference. For scalability, we first compute maximal local approximate matches between scaffolds and reference in distributed manner, and then proceed with co-linear chaining to find a global alignment. Best alignment is removed from the scaffold and the process is iterated with the remaining scaffold content in order to split the scaffold into correctly aligning parts. The proposed normalized N50 metric is then the N50 value computed for the final correctly aligning parts. As a side result of independent interest, we show how to modify co-linear chaining to restrict gaps to produce a more sensible global alignment.


We propose and implement a comprehensive and efficient approach to compute a metric that summarizes scaffold assembly correctness and length. Our implementation can be downloaded from webcite.