Skip to main content

Viral Quasispecies Assembly via Maximal Clique Enumeration

  • Conference paper

Part of the Lecture Notes in Computer Science book series (LNBI,volume 8394)


Genetic variability of virus populations within individual hosts is a key determinant of pathogenesis, virulence, and treatment outcome. It is of clinical importance to identify and quantify the intra-host ensemble of viral haplotypes, called viral quasispecies. Ultra-deep next-generation sequencing (NGS) of mixed samples is currently the only efficient way to probe genetic diversity of virus populations in greater detail. Major challenges with this bulk sequencing approach are (i) to distinguish genetic diversity from sequencing errors, (ii) to assemble an unknown number of different, unknown, haplotype sequences over a genomic region larger than the average read length, (iii) to estimate their frequency distribution, and (iv) to detect structural variants, such as large insertions and deletions (indels) that are due to erroneous replication or alternative splicing. Even though NGS is currently introduced in clinical diagnostics, the de-facto standard procedure to assess the quasispecies structure is still single-nucleotide variant (SNV) calling. Viral phenotypes cannot be predicted solely from individual SNVs, as epistatic interactions are abundant in RNA viruses. Therefore, reconstruction of long-range viral haplotypes has the potential to be adopted, as data is already available.


  • Sequencing Error
  • Viral Phenotype
  • Average Read Length
  • Phred Score
  • Haplotype Sequence

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Buying options

USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-319-05269-4_25
  • Chapter length: 2 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
USD   79.99
Price excludes VAT (USA)
  • ISBN: 978-3-319-05269-4
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   99.99
Price excludes VAT (USA)

Author information

Authors and Affiliations


Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Töpfer, A., Marschall, T., Bull, R.A., Luciani, F., Schönhuth, A., Beerenwinkel, N. (2014). Viral Quasispecies Assembly via Maximal Clique Enumeration. In: Sharan, R. (eds) Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science(), vol 8394. Springer, Cham.

Download citation

  • DOI:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-05268-7

  • Online ISBN: 978-3-319-05269-4

  • eBook Packages: Computer ScienceComputer Science (R0)