The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Open accessAbstract
Abstract The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat ( Capra hircus ), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.
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Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
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
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Self-citationKraken: ultrafast metagenomic sequence classification using exact alignments
Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521
Cited by
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
Self-citationNanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Self-citationCunningham, F., Achuthan, P., Akanni, W., Allen, J., Amode, M. R., Armean, I. M., Bennett, R., Bhai, J., Billis, K., Boddu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1113 · Cited by 925
The Third Revolution in Sequencing Technology
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.008 · Cited by 1,057
De novo assembly of the cattle reference genome with single-molecule sequencing
Rosen, B. D., Bickhart, D. M., Schnabel, R. D., Koren, S., Elsik, C. G., Tseng, E., Rowan, T. N., Low, W. Y., Zimin, A., Couldrey, C., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa021 · Cited by 802
Metadata
- Authors
- Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., Lee, J., Lam, E. T., Liachko, I., Sullivan, S. T., Burton, J. N., Huson, H. J., Nystrom, J. C., Kelley, C. M., Hutchison, J. L., Zhou, Y., Sun, J., Crisà, A., Ponce de León, F. A., Schwartz, J. C., Hammond, J. A., Waldbieser, G. C., Schroeder, S. G., Liu, G. E., Dunham, M. J., Shendure, J., Sonstegard, T. S., Phillippy, A. M., Van Tassell, C. P., & Smith, T. P. L.
- Venue
- Nature Genetics
- Published
- 2017-03-06
- Volume
- 49
- Issue
- 4
- Pages
- 643-650
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2594081754
- Cited by
- 631
- References
- 14
- FWCI
- 29.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., Lee, J., Lam, E. T., Liachko, I., Sullivan, S. T., Burton, J. N., Huson, H. J., Nystrom, J. C., Kelley, C. M., Hutchison, J. L., Zhou, Y., Sun, J., Crisà, A., Ponce de León, F. A., . . . Smith, T. P. L. (2017). Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics. https://doi.org/10.1038/ng.3802
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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