The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
compleasm: a faster and more accurate reimplementation of BUSCO
Open accessAbstract
Motivation: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. Results: Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO’s 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13. Availability and implementation: https://github.com/huangnengCSU/compleasm.
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187
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
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859
Self-citationThe complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136
Self-citationBlobToolKit – Interactive Quality Assessment of Genome Assemblies
Challis, R., Richards, E., Rajan, J., Cochrane, G., & Blaxter, M. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.119.400908 · Cited by 2,610
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Self-citationChallenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A., & Punta, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt263 · Cited by 1,660
Haplotype-resolved assembly of diploid genomes without parental data
Cheng, H., Jarvis, E. D., Fedrigo, O., Koepfli, K.-P., Urban, L., Gemmell, N. J., & Li, H. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01261-x · Cited by 1,038
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Integrated analysis of the complete sequence of a macaque genome
Zhang, S., Xu, N., Fu, L., Yang, X., Ma, K., Li, Y., Yang, Z., Li, Z., Feng, Y., Jiang, X., et al. (2025) · Nature · doi:10.1038/s41586-025-08596-w · Cited by 48
Milia, S., Leonard, A. S., Mapel, X. M., Bernal Ulloa, S. M., Drögemüller, C., & Pausch, H. (2025) · Genome Research · doi:10.1101/gr.279064.124 · Cited by 22
Malovichko, Y. V., Bein, B., Gonzales-Irribarren, A., Leushkin, E., Hilgers, L., Stephen, A., Yi, X., Albertini, M., Stadager, T., Zumpt, M., et al. (2026) · doi:10.64898/2026.06.30.735536 · Cited by 5
Sudasinghe, H., Liu, Z., Triginer-Llabrés, L., Hui Tan, H., Britz, R., Salzburger, W., Peichel, C. L., & Rüber, L. (2026) · doi:10.64898/2026.03.21.713365 · Cited by 2
Metadata
- Authors
- Huang, N., & Li, H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-09-27
- Volume
- 39
- Issue
- 10
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W4387079708
- Cited by
- 333
- References
- 13
- FWCI
- 24.81
- Type
- journal article
- Language
- en
- Open access
- gold
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