Print Email Facebook Twitter HAT Title HAT: haplotype assembly tool using short and error-prone long reads Author Shirali Hossein Zade, R. (TU Delft Pattern Recognition and Bioinformatics) Urhan, A. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard) Assis de Souza, A. (TU Delft Pattern Recognition and Bioinformatics) Singh, A. (TU Delft Electrical Engineering, Mathematics and Computer Science) Abeel, T.E.P.M.F. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard) Faculty Electrical Engineering, Mathematics and Computer Science Date 2022 Abstract MOTIVATION: Haplotypes are the set of alleles co-occurring on a single chromosome and inherited together to the next generation. Because a monoploid reference genome loses this co-occurrence information, it has limited use in associating phenotypes with allelic combinations of genotypes. Therefore, methods to reconstruct the complete haplotypes from DNA sequencing data are crucial. Recently, several attempts have been made at haplotype reconstructions, but significant limitations remain. High-quality continuous haplotypes cannot be created reliably, particularly when there are few differences between the homologous chromosomes. RESULTS: Here, we introduce HAT, a haplotype assembly tool that exploits short and long reads along with a reference genome to reconstruct haplotypes. HAT tries to take advantage of the accuracy of short reads and the length of the long reads to reconstruct haplotypes. We tested HAT on the aneuploid yeast strain Saccharomyces pastorianus CBS1483 and multiple simulated polyploid datasets of the same strain, showing that it outperforms existing tools. AVAILABILITY AND IMPLEMENTATION: https://github.com/AbeelLab/hat/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. To reference this document use: http://resolver.tudelft.nl/uuid:96076582-041e-4d64-9d90-c68cc404af6e DOI https://doi.org/10.1093/bioinformatics/btac702 ISSN 1367-4803 Source Bioinformatics, 38 (24), 5352-5359 Part of collection Institutional Repository Document type journal article Rights © 2022 R. Shirali Hossein Zade, A. Urhan, A. Assis de Souza, A. Singh, T.E.P.M.F. Abeel Files PDF btac702.pdf 793.6 KB Close viewer /islandora/object/uuid:96076582-041e-4d64-9d90-c68cc404af6e/datastream/OBJ/view