The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
LoRDEC: accurate and efficient long read error correction
Open accessAbstract
Motivation: PacBio single molecule real-time sequencing is a third-generation sequencing technique producing long reads, with comparatively lower throughput and higher error rate. Errors include numerous indels and complicate downstream analysis like mapping or de novo assembly. A hybrid strategy that takes advantage of the high accuracy of second-generation short reads has been proposed for correcting long reads. Mapping of short reads on long reads provides sufficient coverage to eliminate up to 99% of errors, however, at the expense of prohibitive running times and considerable amounts of disk and memory space. Results : We present LoRDEC, a hybrid error correction method that builds a succinct de Bruijn graph representing the short reads, and seeks a corrective sequence for each erroneous region in the long reads by traversing chosen paths in the graph. In comparison, LoRDEC is at least six times faster and requires at least 93% less memory or disk space than available tools, while achieving comparable accuracy. Availability and implementaion : LoRDEC is written in C++, tested on Linux platforms and freely available at http://atgc.lirmm.fr/lordec . Contact: lordec@lirmm.fr . Supplementary information: Supplementary data are available at Bioinformatics online.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Navarro, G., & Mäkinen, V. (2007) · ACM Computing Surveys · doi:10.1145/1216370.1216372 · Cited by 735
Improving PacBio Long Read Accuracy by Short Read Alignment
Au, K. F., Underwood, J. G., Lee, L., & Wong, W. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046679 · Cited by 335
Cited by
Weirather, J. L., de Cesare, M., Wang, Y., Piazza, P., Sebastiano, V., Wang, X.-J., Buck, D., & Au, K. F. (2017) · F1000Research · doi:10.12688/f1000research.10571.2 · Cited by 418
Sahraeian, S. M. E., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar, P. T., Au, K. F., Bani Asadi, N., Gerstein, M. B., Wong, W. H., Snyder, M. P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00050-4 · Cited by 376
Ye, C., Hill, C. M., Wu, S., Ruan, J., & Ma, Z. (2016) · Scientific Reports · doi:10.1038/srep31900 · Cited by 304
GraphAligner: rapid and versatile sequence-to-graph alignment
Rautiainen, M., & Marschall, T. (2020) · Genome Biology · doi:10.1186/s13059-020-02157-2 · Cited by 242
A comprehensive evaluation of long read error correction methods
Zhang, H., Jain, C., & Aluru, S. (2020) · BMC Genomics · doi:10.1186/s12864-020-07227-0 · Cited by 150
A reference genome of the Chinese hamster based on a hybrid assembly strategy
Rupp, O., MacDonald, M. L., Li, S., Dhiman, H., Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., et al. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26722 · Cited by 107
Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies
Utturkar, S. M., Klingeman, D. M., Bruno-Barcena, J. M., Chinn, M. S., Grunden, A. M., Köpke, M., & Brown, S. D. (2015) · Scientific Data · doi:10.1038/sdata.2015.14 · Cited by 46
Yao, T., Zhang, Z., Li, Q., Huang, R., Hong, Y., Li, C., Zhang, F., Huang, Y., Fang, Y., Cao, Q., et al. (2023) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-23-0083 · Cited by 22
Metadata
- Authors
- Salmela, L., & Rivals, E.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-08-26
- Volume
- 30
- Issue
- 24
- Pages
- 3506-3514
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2160177274
- Cited by
- 844
- References
- 3
- FWCI
- 9.98
- Type
- journal article
- Language
- en
- Open access
- hybrid
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