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Algoritmi a colazione -- Seminario Nadia Pisanti "WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing"
Relatore: Nadia Pisanti
Dipartimento di Informatica - Universita' di Pisa

Data/Ora/Sede: 4 dicembre 2014, ore 11:00, Sala Riunioni, piano terra
dell'Edificio di Ingegneria dell'Informazione.

Title: "WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing"

The human genome is diploid, which requires to assign heterozygous single
nucleotide polymorphisms (SNPs) to the two copies of the genome. The
resulting haplotypes, lists of SNPs belonging to each copy, are crucial for
downstream analyses in population genetics. Currently, statistical
approaches, which are oblivious to direct read information, constitute the
state-of-the-art. Haplotype assembly, which addresses phasing directly
from sequencing reads, suffers from the fact that sequencing reads of the
current generation are too short to serve the purposes of genome-wide
While future-technology sequencing reads will contain sufficient amounts of
SNPs per read for phasing, they are also likely to suffer from higher
sequencing error rates. Currently, no haplotype assembly approaches exist
that allow for taking both increasing read length and sequencing error
information into account.
Here, we suggest WhatsHap, the first approach that yields provably
optimal solutions to the weighted minimum error correction problem in
runtime linear in the number of SNPs. WhatsHap is a fixed parameter
tractable (FPT) approach with coverage as the parameter. We demonstrate
that WhatsHap can handle datasets of coverage up to 15x, and that 15x
are generally enough for reliably phasing long reads, even at significantly
elevated sequencing error rates. We also find that the switch and flip error
rates of the haplotypes we output are favorable when comparing them with
state-of-the-art statistical phasers.