The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
Open accessAbstract
Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.
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Cites
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
Reducing storage requirements for biological sequence comparison
Roberts, M., Hayes, W., Hunt, B. R., Mount, S. M., & Yorke, J. A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth408 · Cited by 485 · cited 1×
“[15].”
Cited by
Using SPAdes De Novo Assembler
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555
Self-citationPasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591
Single-cell genome sequencing: current state of the science
Gawad, C., Koh, W., & Quake, S. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.16 · Cited by 1,334
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Bushmanova, E., Antipov, D., Lapidus, A., & Prjibelski, A. D. (2019) · GigaScience · doi:10.1093/gigascience/giz100 · Cited by 869
Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life
Reyman, M., van Houten, M. A., van Baarle, D., Bosch, A. A. T. M., Man, W. H., Chu, M. L. J. N., Arp, K., Watson, R. L., Sanders, E. A. M., Fuentes, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13014-7 · Cited by 450
Metadata
- Authors
- Nikolenko, S. I., Korobeynikov, A. I., & Alekseyev, M. A.
- Venue
- BMC Genomics
- Published
- 2013
- Volume
- 14
- Issue
- Suppl 1
- Pages
- S7
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W2075013491
- Cited by
- 479
- References
- 2
- Type
- conference abstract
- Language
- en
- Open access
- gold
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- Nikolenko, S. I., Korobeynikov, A. I., & Alekseyev, M. A. (2013). BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics. https://doi.org/10.1186/1471-2164-14-s1-s7
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