HAT: haplotype assembly tool using short and error-prone long reads.

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.

SUBMITTER: Shirali Hossein Zade R 

PROVIDER: S-EPMC9750119 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature