ORCID Profile
0000-0001-5345-6982
Current Organisation
University of Lausanne
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Publisher: Public Library of Science (PLoS)
Date: 12-06-2020
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 06-2019
Publisher: Cold Spring Harbor Laboratory
Date: 09-01-2020
DOI: 10.1101/2020.01.08.899013
Abstract: Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, there are no algorithms yet for polyploids. The first haplotyping algorithm designed for 10X linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes. Hap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.
Publisher: Springer Science and Business Media LLC
Date: 07-01-2021
Publisher: Springer Science and Business Media LLC
Date: 18-06-2020
DOI: 10.1186/S12859-020-03584-5
Abstract: Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, to the best of our knowledge, no algorithms have yet been proposed for polyploids specifically exploiting linked reads. The first haplotyping algorithm designed for linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes. Hap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.
Publisher: Public Library of Science (PLoS)
Date: 26-03-2019
Location: Iran (Islamic Republic of)
No related grants have been discovered for Sina Majidian.