Mar 20, 2019

GMASS: a novel measure for genome assembly structural similarity

BMC Bioinformatics
Daehong KwonJaebum Kim


Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have been developed to generate high quality de novo assemblies using the NGS reads, but their output is very different because of algorithmic differences. However, there are not properly structured measures to show the similarity or difference in assemblies. We developed a new measure, called the GMASS score, for comparing two genome assemblies in terms of their structure. The GMASS score was developed based on the distribution pattern of the number and coverage of similar regions between a pair of assemblies. The new measure was able to show structural similarity between assemblies when evaluated by simulated assembly datasets. The application of the GMASS score to compare assemblies in recently published benchmark datasets showed the divergent performance of current assemblers as well as its ability to compare assemblies. The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

  • References36
  • Citations1


  • References36
  • Citations1

Mentioned in this Paper

Theoretical Study
Massively-Parallel Sequencing
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Genome, Human
Online Mendelian Inheritance In Man

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