Abstract
There is a growing gap between the generation of massively parallel sequencing output and the ability to process and analyze the resulting data. New users are left to navigate a bewildering maze of base calling, alignment, assembly and analysis tools with often incomplete documentation and no idea how to compare and validate their outputs. Bridging this gap is essential, or the coveted $1,000 genome will come with a $20,000 analysis price tag.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Discovering myeloid cell heterogeneity in the lung by means of next generation sequencing
Military Medical Research Open Access 25 October 2019
-
SePIA: RNA and small RNA sequence processing, integration, and analysis
BioData Mining Open Access 20 May 2016
-
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
BMC Bioinformatics Open Access 10 September 2014
Access options
Subscribe to Journal
Get full journal access for 1 year
$99.00
only $8.25 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Buy article
Get time limited or full article access on ReadCube.
$32.00
All prices are NET prices.
References
Sanger, F., Nicklen, S. & Coulson, A.R. Proc. Natl. Acad. Sci. USA 74, 5463–5467 (1977).
Smith, L.M. et al. Nature 321, 674–679 (1986).
McPherson, J.D. et al. Nature 409, 934–941 (2001).
Lander, E.S. et al. Nature 409, 860–921 (2001).
Kent, W.J. & Haussler, D. Genome Res. 11, 1541–1548 (2001).
Myers, E.W. et al. Science 287, 2196–2104 (2000).
Huson, D.H. et al. Bioinformatics 17 (suppl. 1), S132–S139 (2001).
Venter, J.C. et al. Science 291, 1304–1351 (2001).
Kent, W.J. et al. Genome Res. 12, 996–1006 (2002).
Hubbard, T. et al. Nucleic Acids Res. 30, 38–41 (2002).
Wheeler, D.L. et al. Nucleic Acids Res. 29, 11–16 (2001).
Bhangale, T.R., Stephens, M. & Nickerson, D.A. Nat. Genet. 38, 1457–1462 (2006).
Chen, K. et al. Genome Res. 17, 659–666 (2007).
Zhang, J. et al. PLoS Comput. Biol. 1, e53 395–404 (2005).
Margulies, M. et al. Nature 437, 376–380 (2005).
Mardis, E. Annu. Rev. Genomics Hum. Genet. 9, 387–402 (2008).
Turner, D.J., Keane, T.M., Sudbery, I. & Adams, D.J. Mamm. Genome 20, 327–338 (2009).
Edwards, R.A. et al. BMC Genomics 7, 57 (2006).
Goldberg, S.M. et al. Proc. Natl. Acad. Sci. USA 103, 11240–11245 (2006).
Girard, A., Sachidanandam, R., Hannon, G.J. & Carmell, M.A. Nature 442, 199–202 (2006).
Binladen, J. et al. PLoS One 2, e197 (2007).
Velculescu, V.E. et al. Science 270, 484–487 (1995).
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Nat. Methods 5, 621–628 (2008).
Nielsen, K.L., Høgh, A.L. & Emmersen, J. Nucleic Acids Res. 34, e133 (2006).
Robertson, G. et al. Nat. Methods 4, 651–657 (2007).
Xie, C. & Tammi, M.T. BMC Bioinformatics 10, 80 (2009).
Mortazavi, A. & Wold, B. Nat. Methods 6, S21–S31 (2009).
Medvedev, P., Stanciu, M. & Brudno, M. Nat. Methods 6, S13–S20 (2009).
Flicek, P. & Birney, E. Nat. Methods 6, S6–S12 (2009).
Simpson, J.T. et al. Genome Res. 19, 1117–1123 (2009).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The author declares no competing financial interests.
Rights and permissions
About this article
Cite this article
McPherson, J. Next-generation gap. Nat Methods 6 (Suppl 11), S2–S5 (2009). https://doi.org/10.1038/nmeth.f.268
Published:
Issue Date:
DOI: https://doi.org/10.1038/nmeth.f.268
This article is cited by
-
Discovering myeloid cell heterogeneity in the lung by means of next generation sequencing
Military Medical Research (2019)
-
Advances of genotyping-by-sequencing in fisheries and aquaculture
Reviews in Fish Biology and Fisheries (2017)
-
SePIA: RNA and small RNA sequence processing, integration, and analysis
BioData Mining (2016)
-
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
BMC Bioinformatics (2014)
-
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)
BMC Genomics (2013)