Identifying and removing haplotypic duplication in primary genome assemblies

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 rath...

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Vydáno v:Bioinformatics Ročník 36; číslo 9; s. 2896 - 2898
Hlavní autoři: Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 01.05.2020
Témata:
Applications Notes
Genome
Haplotypes
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Software
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
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Shrnutí: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 focus only 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 current tools, 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 easily be integrated into assembly pipelines. Availability and implementation The source code is written in C and is available at https://github.com/dfguan/purge_dups. Supplementary information Supplementary data are available at Bioinformatics online.
Bibliografie:ObjectType-Article-1
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btaa025