Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies Arang Rhie* , Brian P. Walenz, Sergey Koren and Adam M. Phillippy * Correspondence: arang.rhie@nih. gov Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Abstract Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. Multiple visualizations, such as k-mer spectrum plots, can be generated for evaluation. We demonstrate on both human and plant genomes that Merqury is a fast and robust method for assembly validation. Keywords: Genome assembly, Assembly validation, Benchmarking, K-mers, Haplotype phasing, Trio binning
Background With recent advances in long-read [1–3] and long-range sequencing technologies [4–6], new assembly pipelines are generating more continuous, complete, and accurate diploid genome assemblies than ever before [4, 7–14]. However, de novo assembled genomes are difficult to validate due to the lack of a known truth. Existing methods use Illumina reads to infer base-level accuracy by aligning the reads to the assembly for evaluation [15]. Base errors in the consensus are detected as variants (SNPs or small indels) when aligning the short reads. However, this method is heavily reliant on the short-read mapping, which could be biased in repetitive regions, under-collapsed regions, or regions of low consensus accuracy. For measuring completeness and false duplications, near-universal single-copy orthologs (BUSCOs) [16] have been widely used to evaluate the gene content of assemblies. BUSCO is robust for species that have been widely studied, such as human and mouse. However, this analysis can be inaccurate when the newly assembled genome contains true copy number or sequence variants that were not considered when building the © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the
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