TY - JOUR AU - Bracciali, Andrea AU - Aldinucci, Marco AU - Patterson, Murray AU - Marschall, Tobias AU - Pisanti, Nadia AU - Merelli, Ivan AU - Torquati, Massimo PY - 2016 DA - 2016/09/22 TI - PWHATSHAP: efficient haplotyping for future generation sequencing JO - BMC Bioinformatics SP - 342 VL - 17 IS - 11 AB - Haplotype phasing is an important problem in the analysis of genomics information. Given a set of DNA fragments of an individual, it consists of determining which one of the possible alleles (alternative forms of a gene) each fragment comes from. Haplotype information is relevant to gene regulation, epigenetics, genome-wide association studies, evolutionary and population studies, and the study of mutations. Haplotyping is currently addressed as an optimisation problem aiming at solutions that minimise, for instance, error correction costs, where costs are a measure of the confidence in the accuracy of the information acquired from DNA sequencing. Solutions have typically an exponential computational complexity. WhatsHap is a recent optimal approach which moves computational complexity from DNA fragment length to fragment overlap, i.e., coverage, and is hence of particular interest when considering sequencing technology’s current trends that are producing longer fragments. SN - 1471-2105 UR - https://doi.org/10.1186/s12859-016-1170-y DO - 10.1186/s12859-016-1170-y ID - Bracciali2016 ER -