ReHap - Reconstruct Haplotypes

ReHap - Reconstruct Haplotypes, is a web application aiming to provide users with a common interface to five algorithms for the parental haplotype reconstruction problem (also known as Haplotyping Assembly Problem).
ReHap allows you to: generate a matrix of fragments simulating the shotgun sequencing procedure coming from real human haplotypes from HapMap project; run up to five state of the art algorithms for the parental haplotype reconstruction; view the SNP matrix highlighting errors, the original haplotype strands and the reconstructed solutions; compare algorithms solutions with the ground truth; upload user data.
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How to use ReHap
The ReHap interface is divided in four tabs. The first tab allows to set all the parameters for the SNP matrix generator. The second tab provides a simple interface to inspect the generated haplotypes and SNP matrix. Implanted errors are highlighted to be better identified. The third tab gives the possibility to select the algorithms and to set their parameters. To finish, the last tab provides a simple way to compare the results of all the selected algorithms.
The SNP matrix is generated according to a certain number of parameters. Among them: the haplotypes length, the error rate, the coverage and whether to insert gaps in the matrix or not. It is possible to select one of the chromosomes of a certain individual among four different populations from the HapMap Project. It is also possible to generate the SNP matrix starting from user haplotyping data. The generation process simulate the shotgun sequencing process according with the description in CelSim. Default parameters reflect actual technology.
ReHap allows to run five algorithms: SpeedHap is an algorithm developed in our labs. Fast Hare is a well known heuristic algorithm for the parental haplotyping problem MLF is a randomized algorithm that attempts to minimize the MEC (Minimum Error Correction) objective function 2 distance MAC: is a clustering algorithm that combine two distance definition to split fragments in two clusters SHR-3 use a probabilistic approach to the MFR (Minimum Fragment Removal) problem in order to reconstruct the haplotypes
References:
Speedhap: An accurate heuristic for the single individual SNP haplotyping problem with many gaps, high reading error rate and low coverage L.M. Genovese, F. Geraci, and M. Pellegrini EEE/ACM Transactions on Computational Biology and Bioinformatics, 2008
Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments Zhixiang Chen and Bin Fu and Robert T. Schweller and Boting Yang and Zhiyu Zhao and Binhai Zhu APBC - Imperial College Press, 2008
A clustering algorithm based on two distance functions for MEC model Y. Wang, E. Feng, and R. Wang Computational Biology and Chemistry , 2007
Haplotype assembly from aligned weighted SNP fragments Y.Y. Zhao, L.Y. Wu, J.H. Zhang, R.S. Wang, and X.S. Zhang Computational Biology and Chemistry, 2005
Fast hare: A fast heuristic for single individual SNP haplotype reconstruction A. Panconesi and M. Sozio Proc. WABI, 2004
A dataset generator for whole genome shotgun sequencing G. Myers International Conference on Intelligent Systems for Molecular Biology, 1999
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