The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
LUMPY: a probabilistic framework for structural variant discovery
Open accessAbstract
Comprehensive discovery of structural variation (SV) from whole genome sequencing data requires multiple detection signals including read-pair, split-read, read-depth and prior knowledge. Owing to technical challenges, extant SV discovery algorithms either use one signal in isolation, or at best use two sequentially. We present LUMPY, a novel SV discovery framework that naturally integrates multiple SV signals jointly across multiple samples. We show that LUMPY yields improved sensitivity, especially when SV signal is reduced owing to either low coverage data or low intra-sample variant allele frequency. We also report a set of 4,564 validated breakpoints from the NA12878 human genome. https://github.com/arq5x/lumpy-sv.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Self-citationAbyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011) · Genome Research · doi:10.1101/gr.114876.110 · Cited by 1,658
Genome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630 · cited 1×
“spanning paired-end reads that align discordantly relative to each other (read-pair), and breakpoint-containing single reads that align in split fashion to discontiguous loci in the reference genome (split-read) [1,2].”
BackgroundMapping copy number variation by population-scale genome sequencing
1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140 · cited 10×
“The read-pair module maps the output of a paired-end sequence alignment algorithm such as NOVOALIGN (C Hercus, unpublished) [8] or BWA [9], the split-read module maps the output of a split-read sequence alignment algorithm (for example, YAHA [10], BWA-SW [11], or BWA-MEM [5]), and the generic module allows users to in…”
BackgroundMethodInfluential
Cited by
(2015) · doi:10.1093/bioinformatics/btv710 · Cited by 2,234
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Self-citationChapuy, B., Stewart, C., Dunford, A. J., Kim, J., Kamburov, A., Redd, R. A., Lawrence, M. S., Roemer, M. G. M., Li, A. J., Ziepert, M., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0016-8 · Cited by 1,941
Versatile genome assembly evaluation with QUAST-LG
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty266 · Cited by 1,527
Next-Generation Sequencing Technology: Current Trends and Advancements
Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R. P., Banday, S., Mishra, A. K., Das, G., et al. (2023) · Biology · doi:10.3390/biology12070997 · Cited by 1,299
Metadata
- Authors
- Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M.
- Venue
- Genome Biology
- Published
- 2014-06-26
- Volume
- 15
- Issue
- 6
- Pages
- R84-R84
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2111350087
- Cited by
- 1,554
- References
- 6
- FWCI
- 38.24
- Type
- journal article
- Language
- en
- Open access
- gold
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- Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014). LUMPY: a probabilistic framework for structural variant discovery. Genome Biology. https://doi.org/10.1186/gb-2014-15-6-r84
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