The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
ALLMAPS: robust scaffold ordering based on multiple maps
Open accessAbstract
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.
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Cites
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Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
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“Genome assembly can also be greatly improved using genetic mapping populations to create a linkage map (Fierst 2015) and/ or through optical mapping that places scaffolds on chromosomes (Sharma et al. 2013; Tang et al. 2015 a , 2015 b ; VanBuren et al. 2015).”
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
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RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B., & Schatz, M. C. (2019) · Genome Biology · doi:10.1186/s13059-019-1829-6 · Cited by 685
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Self-citationPearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3943 · Cited by 513
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Metadata
- Authors
- Tang, H., Zhang, X., Miao, C., Zhang, J., Ming, R., Schnable, J. C., Schnable, P. S., Lyons, E., & Lu, J.
- Venue
- Genome Biology
- Published
- 2015-01-13
- Volume
- 16
- Issue
- 1
- Pages
- 3-3
- ISSN
- 1465-6906 (ISSN-L)
- OpenAlex
- W2153218781
- Cited by
- 388
- References
- 39
- FWCI
- 9.13
- Type
- journal article
- Language
- en
- Open access
- gold
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