The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Open accessAbstract
Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish microbial genomes, but available assembly methods have not scaled well to larger genomes. We introduce the MinHash Alignment Process (MHAP) for overlapping noisy, long reads using probabilistic, locality-sensitive hashing. Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and a human hydatidiform mole cell line (CHM1) from SMRT sequencing. The resulting assemblies are highly continuous, include fully resolved chromosome arms and close persistent gaps in these reference genomes. Our assembly of D. melanogaster revealed previously unknown heterochromatic and telomeric transition sequences, and we assembled low-complexity sequences from CHM1 that fill gaps in the human GRCh38 reference. Using MHAP and the Celera Assembler, single-molecule sequencing can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.
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BackgroundIdentifying and Filtering Near-Duplicate Documents
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Cited by
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
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Assembly of long, error-prone reads using repeat graphs
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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
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Self-citationMash: fast genome and metagenome distance estimation using MinHash
Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., & Phillippy, A. M. (2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373
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Metadata
- Authors
- Berlin, K., Koren, S., Chin, C.-S., Drake, J. P., Landolin, J. M., & Phillippy, A. M.
- Venue
- Nature Biotechnology
- Published
- 2015-05-25
- Volume
- 33
- Issue
- 6
- Pages
- 623-630
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1579534339
- Cited by
- 934
- References
- 8
- FWCI
- 52.75
- Type
- journal article
- Language
- en
- Open access
- green
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