The low cost of short-read sequencing has motivated the development of de novo assemblies from only short-read data; impressively, assemblies for large mammalian genomes are now available. However, this is still a developing field, and these de novo assemblies have many artifacts, as do all de novo assemblies.
This is a preview of subscription content, log in via an institution to check access.
References
Alkan, C., Sajjadian, S. & Eichler, E.E. Nat. Methods 8, 61–65 (2011).
Li, R. et al. Genome Res. 20, 265–272 (2009).
Miller, J.R., Koren, S. & Sutton, G. Genomics 95, 315–327 (2010).
Salzberg, S.L. & Yorke, J.A. Bioinformatics 21, 4320–4321 (2005).
1000 Genomes Project Consortium. Nature 467, 1061–1073 (2010).
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
Birney, E. Assemblies: the good, the bad, the ugly. Nat Methods 8, 59–60 (2011). https://doi.org/10.1038/nmeth0111-59
Published:
Issue Date:
DOI: https://doi.org/10.1038/nmeth0111-59
- Springer Nature America, Inc.
This article is cited by
-
OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Genome Biology (2016)
-
Close ecological relationship among species facilitated horizontal transfer of retrotransposons
BMC Evolutionary Biology (2016)
-
Clustering of reads with alignment-free measures and quality values
Algorithms for Molecular Biology (2015)
-
Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly
BMC Genomics (2014)
-
Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology
BMC Genomics (2013)