The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Current challenges in de novo plant genome sequencing and assembly
Open accessAbstract
Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.
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Citations
Cites
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
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
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 2×
“Several short-read assembly packages have been proven for mammalian-sized genomes up to the 3 Gbp human genome, including ABySS [51], ALLPATHS-LG [31], the Celera Assembler [52,53], Newbler [54], SGA [55] and SOAPdenovo [56].”
The Global Carbon Cycle: A Test of Our Knowledge of Earth as a System
Falkowski, P., Scholes, R. J., Boyle, E., Canadell, J., Canfield, D., Elser, J., Gruber, N., Hibbard, K., Högberg, P., Linder, S., et al. (2000) · Science · doi:10.1126/science.290.5490.291 · Cited by 2,177
Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Ann Blomberg, L., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000475 · Cited by 416
Self-citation
Cited by
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530
Self-citationKAT: 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
A field guide to whole‐genome sequencing, assembly and annotation
Ekblom, R., & Wolf, J. B. W. (2014) · Evolutionary Applications · doi:10.1111/eva.12178 · Cited by 428
Machine learning: a powerful tool for gene function prediction in plants
Mahood, E. H., Kruse, L. H., & Moghe, G. D. (2020) · Applications in Plant Sciences · doi:10.1002/aps3.11376 · Cited by 153
Metadata
- Authors
- Schatz, M. C., Witkowski, J., & McCombie, W. R.
- Venue
- Genome Biology
- Published
- 2012
- Volume
- 13
- Issue
- 4
- Pages
- 243
- ISSN
- 1465-6906 (ISSN-L)
- OpenAlex
- W2154420975
- Cited by
- 185
- References
- 6
- FWCI
- 7.20
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
