This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Image-centric compression of protein structures improves space savings
BMC Bioinformatics Open Access 21 November 2023
-
IonCRAM: a reference-based compression tool for ion torrent sequence files
BMC Bioinformatics Open Access 09 September 2020
-
Performance evaluation of lossy quality compression algorithms for RNA-seq data
BMC Bioinformatics Open Access 20 July 2020
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Berger, B., Peng, J. & Singh, M. Nat. Rev. Genet. 14, 333–346 (2013).
Kahn, S.D. Science 331, 728–729 (2011).
The 1000 Genomes Project Consortium. Nature 491, 56–65 (2012).
Veeramah, K.R. & Hammer, M.F. Nat. Rev. Genet. 15, 149–162 (2014).
Shapiro, E., Biezuner, T. & Linnarsson, L. Nat. Rev. Genet. 14, 618–630 (2013).
Bonfield, J.K. & Mahoney, M.V. PLoS ONE 8, e59190 (2013).
Apostolico, A. & Lonardi, S. in Proceedings of the IEEE Data Compression Conference 2000 (DCC'00) 143–152 (IEEE Computer Society, 2000).
Kozanitis, C., Saunders, C., Kruglyak, S., Bafna, V. & Varghese, G. J. Comput. Biol. 18, 401–413 (2011).
Jones, D.C., Ruzzo, W.L., Peng, X. & Katze, M.G. Nucleic Acids Res. 40, e171 (2012).
Fritz, M.H.Y., Leinonen, R., Cochrane, G. & Birney, E. Genome Res. 21, 734–740 (2011).
Deorowicz, S. & Grabowski, S. Bioinformatics 27, 860–862 (2011).
Loh, P.R., Baym, M. & Berger, B. Nat. Biotechnol. 30, 627–630 (2012).
Ochoa, I. et al. BMC Bioinformatics 14, 187 (2013).
Hach, F., Numanagic, I., Alkan, C. & Sahinalp, S.C. Bioinformatics 28, 3051–3057 (2012).
Christley, S., Lu, Y., Li, C. & Xie, X. Bioinformatics 25, 274–275 (2009).
Janin, L., Rosone, G. & Cox, A.J. Bioinformatics 30, 24–30 (2014).
DePristo, M.A. et al. Nat. Genet. 43, 491–498 (2011).
Yu, Y.W., Yorukoglu, D. & Berger, B. in Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014—Proceedings (ed. Sharan, R.) 385–399 (Springer, 2014).
Kelley, D.R., Schatz, M.C. & Salzberg, S.L. Genome Biol. 11, R116 (2010).
Grabherr, M.G. et al. Nat. Biotechnol. 29, 644–652 (2011).
Cánovas, R., Moffat, A. & Turpin, A. Bioinformatics 30, 2130–2136 (2014).
Li, H. et al. Bioinformatics 25, 2078–2079 (2009).
Li, H. & Durbin, R. Bioinformatics 26, 589–595 (2010).
Langmead, B. & Salzberg, S.L. Nat. Methods 9, 357–359 (2012).
Acknowledgements
We thank L. Cowen and N. Daniels for helpful discussions and comments. Y.W.Y. gratefully acknowledges support from the Fannie and John Hertz Foundation. D.Y., J.P. and B.B. are partially supported by US National Institutes of Health grant GM108348.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Figures and Text
Supplementary Figures 1–12, Supplementary Tables 1–6 and Supplementary Methods (PDF 889 kb)
Supplementary Code
Source code for the Quartz software described and used in the manuscript (ZIP 23 kb)
Rights and permissions
About this article
Cite this article
Yu, Y., Yorukoglu, D., Peng, J. et al. Quality score compression improves genotyping accuracy. Nat Biotechnol 33, 240–243 (2015). https://doi.org/10.1038/nbt.3170
Published:
Issue Date:
DOI: https://doi.org/10.1038/nbt.3170
This article is cited by
-
Image-centric compression of protein structures improves space savings
BMC Bioinformatics (2023)
-
IonCRAM: a reference-based compression tool for ion torrent sequence files
BMC Bioinformatics (2020)
-
Performance evaluation of lossy quality compression algorithms for RNA-seq data
BMC Bioinformatics (2020)
-
Better quality score compression through sequence-based quality smoothing
BMC Bioinformatics (2019)
-
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph
BMC Bioinformatics (2015)