Next-generation sequence assembly: four stages of data processing and computational challenges

PLoS Comput Biol. 2013;9(12):e1003345. doi: 10.1371/journal.pcbi.1003345. Epub 2013 Dec 12.


Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we address the basic framework of next-generation genome sequence assemblers, which comprises four basic stages: preprocessing filtering, a graph construction process, a graph simplification process, and postprocessing filtering. Here we discuss them as a framework of four stages for data analysis and processing and survey variety of techniques, algorithms, and software tools used during each stage. We also discuss the challenges that face current assemblers in the next-generation environment to determine the current state-of-the-art. We recommend a layered architecture approach for constructing a general assembler that can handle the sequences generated by different sequencing platforms.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Base Sequence
  • DNA / chemistry*
  • Genome
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*
  • Software


  • DNA

Grant support

This work was supported by Japan Society for Promotion of Science (JSPS) Grants-in-Aid for Scientific Research [No. 236172] and the Egyptian Ministry of Higher Education, the Egyptian Bureau of Culture, Science and Education - Tokyo to MH; and Google Anita Borg Memorial Scholarship to SE The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.