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.
- Armin Töpfer
- Tobias Marschall
- Maryam Zaheri
- Bernhard Lang
- Marcel Meyerheim
- The HaploClique implementation was derived from CLEVER
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