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Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
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README.md

HaploClique

We present a novel method to reconstruct the structure of a viral quasispecies from NGS data. Our approach can be used to:

  • reconstruct local error-corrected haplotypes and estimate their abundance
  • assemble full-length viral haplotypes
  • detect large deletions and insertions from paired-end data.

Reference implementation of:

Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, and Niko Beerenwinkel. Viral quasispecies assembly via maximal clique finding PLOS Computational Biology, 2014.

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