The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Versatile genome assembly evaluation with QUAST-LG
Open accessAbstract
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 Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Cutadapt removes adapter sequences from high-throughput sequencing reads
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Self-citationMinimap2: Pairwise alignment for nucleotide sequences
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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QUAST: quality assessment tool for genome assemblies
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Self-citationCircos: An information aesthetic for comparative genomics
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Assembly of long, error-prone reads using repeat graphs
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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Cited by
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
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YaHS: yet another Hi-C scaffolding tool
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A draft human pangenome reference.
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“QUAST was invoked with the following command: python /opt/quast/quast-5.”
MethodInfluentialmetaFlye: scalable long-read metagenome assembly using repeat graphs
Kolmogorov, M., Bickhart, D. M., Behsaz, B., Gurevich, A., Rayko, M., Shin, S. B., Kuhn, K., Yuan, J., Polevikov, E., Smith, T. P. L., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-00971-x · Cited by 1,077
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Metadata
- Authors
- Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-06-27
- Volume
- 34
- Issue
- 13
- Pages
- i142-i150
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2808352813
- Cited by
- 1,527
- References
- 52
- FWCI
- 23.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
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