The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
Open accessAbstract
The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/.
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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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 1×
“In general, a 64 GB memory is a minimum requirement for subsequent large-scale data analysis using popular tools such as Velvet [31], SOAPdenovo [32], ALLPATHS-LG [33] and so on.”
MethodThe sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
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Conceição-Neto, N., Zeller, M., Lefrère, H., De Bruyn, P., Beller, L., Deboutte, W., Yinda, C. K., Lavigne, R., Maes, P., Ranst, M. V., et al. (2015) · Scientific Reports · doi:10.1038/srep16532 · Cited by 363
Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality
Shih, H.-Y., Sciumè, G., Mikami, Y., Guo, L., Sun, H.-W., Brooks, S. R., Urban, J. F., Davis, F. P., Kanno, Y., & O’Shea, J. J. (2016) · Cell · doi:10.1016/j.cell.2016.04.029 · Cited by 334
Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation
Nagashima, H., Mahlakõiv, T., Shih, H.-Y., Davis, F. P., Meylan, F., Huang, Y., Harrison, O. J., Yao, C., Mikami, Y., Urban, J. F., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.06.009 · Cited by 322
FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age
García-Prat, L., Perdiguero, E., Alonso-Martín, S., Dell’Orso, S., Ravichandran, S., Brooks, S. R., Juan, A. H., Campanario, S., Jiang, K., Hong, X., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-00593-7 · Cited by 161
Cai, N., Gomez-Duran, A., Yonova-Doing, E., Kundu, K., Burgess, A. I., Golder, Z. J., Calabrese, C., Bonder, M. J., Camacho, M., Lawson, R. A., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01441-3 · Cited by 73
Metadata
- Authors
- Xu, H., Luo, X., Qian, J., Pang, X., Song, J., Qian, G., Chen, J., & Chen, S.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-12-20
- Volume
- 7
- Issue
- 12
- Pages
- e52249
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2086399100
- Cited by
- 619
- References
- 5
- FWCI
- 2.21
- Type
- journal article
- Language
- en
- Open access
- gold
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- Xu, H., Luo, X., Qian, J., Pang, X., Song, J., Qian, G., Chen, J., & Chen, S. (2012). FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads. PLoS ONE. https://doi.org/10.1371/journal.pone.0052249
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