The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
Open accessAbstract
Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.
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Cites
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“Trimming has been broadly adopted in most recent NGS studies, specifically prior to genome assembly [23], transcriptome assembly [24], metagenome reconstruction [25], RNA-Seq [26,27], epigenetic studies [7] and comparative genomics [28].”
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Cited by
Meng, J., Lu, Z., Liu, H., Zhang, L., Zhang, S., Chen, Y., Rao, M. K., & Huang, Y. (2014) · Methods · doi:10.1016/j.ymeth.2014.06.008 · Cited by 375
A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
Canaguier, A., Grimplet, J., Di Gaspero, G., Scalabrin, S., Duchêne, E., Choisne, N., Mohellibi, N., Guichard, C., Rombauts, S., Le Clainche, I., et al. (2017) · Genomics Data · doi:10.1016/j.gdata.2017.09.002 · Cited by 322
Self-citationBranstetter, M. G., Longino, J. T., Ward, P. S., & Faircloth, B. C. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12742 · Cited by 308
Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240
Next-generation data filtering in the genomics era
Hemstrom, W., Grummer, J. A., Luikart, G., & Christie, M. R. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00738-6 · Cited by 77
Metadata
- Authors
- Del Fabbro, C., Scalabrin, S., Morgante, M., & Giorgi, F. M.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-12-23
- Volume
- 8
- Issue
- 12
- Pages
- e85024
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W1983426138
- Cited by
- 475
- References
- 12
- FWCI
- 9.82
- Type
- journal article
- Language
- en
- Open access
- gold
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