NucMerge: Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads

Background In spite of the major breakthroughs in the second-generation sequencing technologies and the developments of a plethora of assemblers over the last ten years, the resulting genome assemblies may still be fragmented and contain errors. It is typical in genome projects with second-generation reads involved to run multiple assemblers with different parameters and choose the best assembly. However, such an approach is always a trade-off between the strengths and weaknesses of the assemblies. To exploit the advantages of different assemblers, an alternative approach that combines the best parts of several assemblies into one may be applied. The existing tools based on such an approach assist in elongation of assembly fragments and/or improvement of assembly accuracy. Though there has been progress with such a strategy, there is still room for improvement of the existing tools.

Results We present NucMerge, a tool for improving genome assembly accuracy by incorporating information derived from an alternative assembly and paired-end Illumina reads from the same genome. The tool corrects insertion, deletion, substitution, and inversion errors and locates different inter- and intra-chromosomal rearrangement errors. NucMerge was compared to two existing alternatives, namely Metassembler and GAM-NGS.

Conclusions The benchmarking results show that NucMerge has generally better performance than the other tools tested, providing accuracy improvement of more assemblies. NucMerge is freely available at https://github.com/uio-bmi/NucMerge under the MPL license.