Versatile genome assembly evaluation with QUAST-LG

By Alla Mikheenko, Andrey D. Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey A. Gurevich. Bioinform., 2018

1,284 citations recorded by the source corpus.

Motivation The emergence of high‐throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long‐read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian‐size genomes. Results In this manuscript, we demonstrate performance of the state‐of‐the‐art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST‐LG—a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST‐LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference. Availability and implementation http://cab.spbu.ru/software/quast‐lg

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ad449e6506727c4d5efa9c73f88e46463500f7f1

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Citations in the corpus

Assembly of long, error-prone reads using repeat graphs (2018, methodology): “To provide a fair comparison between all three assem-blers using QUAST, we thus modified the hg38 reference by masking the centromeric regions using the coordinates from the UCSC Genome Browser.”
A draft human pangenome reference (2022, methodology): “QUAST was invoked with the following command: python /opt/quast/quast-5.”
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020, methodology): “QUAST-LG [18] is another assembly validation tool that provides both BUSCO and reference-based k-mer measurements, as well as alignment metrics against a closely related reference genome.”