Identifying and removing haplotypic duplication in primary genome assemblies

By Dengfeng Guan, Shane A. McCarthy, Jonathan M. D. Wood, Kerstin Howe, Yadong Wang, Richard Durbin. bioRxiv, 2019

2,457 citations recorded by the source corpus.

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

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ddda566726d4c93b8958147ae8d2e7c0ccbf127b

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Citations in the corpus

Significantly improving the quality of genome assemblies through curation (2020, positive): “False duplications can be removed, ideally after generating the contigs, with tools that recognise partial and complete allele overlap, such as purge_dups [15].”
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, positive): “We then used purge_dups to compute and visualize the contig coverage distribution, and we determined that haplotypic duplication was not evident in the screened contigs [32].”
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, methodology): “Canu also does not assign contigs to haplotypes and requires postprocessing with a tool such as Purge_dups (Guan et al. 2020) to split the diploid assembly into primary and alternate alleles.”
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, positive): “We then used purge_dups to compute and visualize the contig coverage distribution, and we determined that haplotypic duplication was not evident in the screened contigs [45].”