The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Identifying and removing haplotypic duplication in primary genome assemblies
Open accessAbstract
Motivation: Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors. Results: Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines. Availability and implementation: The source code is written in C and is available at https://github.com/dfguan/purge_dups. Supplementary information: Supplementary data are available at Bioinformatics online.
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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
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,304
Phased diploid genome assembly with single-molecule real-time sequencing
Chin, C.-S., Peluso, P., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,904
GenomeScope: fast reference-free genome profiling from short reads
Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., & Schatz, M. C. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx153 · Cited by 1,839
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Li, H. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw152 · Cited by 1,508
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2485-7 · Cited by 1,148
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
Mapleson, D., Garcia Accinelli, G., Kettleborough, G., Wright, J., & Clavijo, B. J. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw663 · Cited by 538
Redundans: an assembly pipeline for highly heterozygous genomes
Pryszcz, L. P., & Gabaldón, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw294 · Cited by 522
Huang, S., Kang, M., & Xu, A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx220 · Cited by 191
Cited by
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
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Self-citationTowards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Self-citationSignificantly improving the quality of genome assemblies through curation
Howe, K., Chow, W., Collins, J., Pelan, S., Pointon, D.-L., Sims, Y., Torrance, J., Tracey, A., & Wood, J. (2021) · GigaScience · doi:10.1093/gigascience/giaa153 · Cited by 2,090
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Metadata
- Authors
- Guan, D., McCarthy, S. A., Wood, J., Howe, K., Wang, Y., & Durbin, R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-01-23
- Volume
- 36
- Issue
- 9
- Pages
- 2896-2898
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W3002362821
- Cited by
- 2,706
- References
- 13
- FWCI
- 68.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
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