The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Scaffolding of long read assemblies using long range contact information
Open accessAbstract
BACKGROUND: Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually does not reconstruct a full chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To increase the contiguity of the assembly to the chromosome level, different strategies are used which exploit long range contact information between chromosomes in the genome. METHODS: We develop a scalable and computationally efficient scaffolding method that can boost the assembly contiguity to a large extent using genome-wide chromatin interaction data such as Hi-C. RESULTS: we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies. We tested our methods on the human and goat genome assemblies. We compare our scaffolds with the scaffolds generated by LACHESIS based on various metrics. CONCLUSION: Our new algorithm SALSA produces more accurate scaffolds compared to the existing state of the art method LACHESIS.
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Cites
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Cited by
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
Significantly improving the quality of genome assemblies through curation
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Piercing the dark matter: bioinformatics of long-range sequencing and mapping
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Ancient gene linkages support ctenophores as sister to other animals
Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362
Metadata
- Authors
- Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C.-S.
- Venue
- BMC Genomics
- Published
- 2017-07-12
- Volume
- 18
- Issue
- 1
- Pages
- 527-527
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W2952020649
- Cited by
- 304
- References
- 46
- FWCI
- 5.05
- Type
- journal article
- Language
- en
- Open access
- gold
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