Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
By Arang Rhie, Brian Walenz, Sergey Koren, Adam M. Phillippy. Genome Biology, 2020
3,144 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/20fee22f5b719e14256d670a1cb37ae6740a2786
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In Molecular Biology
- Heng Li
- Steven L. Salzberg
- Sergey Koren
- Adam M. Phillippy
- Michael C. Schatz
- Fritz J. Sedlazeck
- Mark J. P. Chaisson
- Richard Durbin
Citations in the corpus
- Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, positive): “Mercury was used to calculate QV and k-mer completeness metrics [44].”
- A draft human pangenome reference (2022, methodology): “Assembly QV was also determined using Meryl and Merqury (Rhie et al., 2020).”
- HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, methodology): “Per-base consensus accuracy was estimated using Merqury (Rhie et al. 2020) with Illumina sequencing data from the D. melanogaster F1 parental strains (Supplemental Table S2; Supplemental Note 2).”
- Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, positive): “Merqury was used to calculate QV and k-mer completeness metrics using 21-mers from the HiFi data [55].”
- The complete sequence of a human genome (2021, methodology): “2 by Merqury (81) based on the analysis of 21-mer spectra from the combination of HiFi and PCR-free Illumina reads (after filtering low copy-count 21-mers, for details see (34)).”