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.

Documentation

• Installation
• Usage

Contributions

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

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