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Identifying andremoving haplotypicduplication inprimary genomeassemblies Dengfeng GuanShane McCarthyJonathan Wood2019 год

Identifying and removing haplotypic duplication in primary genome assemblies
preprint

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Аннотация: Abstract Motivation Rapid development in long read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either only focus on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors. Results Here we present a novel tool “purge_dups” that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with the current standard, purge_haplotigs, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can be easy integrated into assembly pipelines. Availability The source code is written in C and is available at https://github.com/dfguan/purge_dups . Contact ydwang@hit.edu.cn , rd109@cam.ac.uk
Год издания: 2019
Авторы: Dengfeng Guan, Shane McCarthy, Jonathan Wood, Kerstin Howe, Yadong Wang, Richard Durbin
Издательство: Cold Spring Harbor Laboratory
Источник: bioRxiv (Cold Spring Harbor Laboratory)
Ключевые слова: Genomics and Phylogenetic Studies, Protist diversity and phylogeny, RNA and protein synthesis mechanisms
Другие ссылки: bioRxiv (Cold Spring Harbor Laboratory) (PDF)
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academic.oup.com (PDF)
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Apollo (University of Cambridge) (PDF)
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