4.8 Article

Limitations of next-generation genome sequence assembly

Journal

NATURE METHODS
Volume 8, Issue 1, Pages 61-65

Publisher

NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.1527

Keywords

-

Funding

  1. US National Institutes of Health [HG002385]
  2. Howard Hughes Medical Institute
  3. NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG002385] Funding Source: NIH RePORTER

Ask authors/readers for more resources

High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short oligonucleotide analysis package (SOAP), generated from the genomes of a Han Chinese individual and a Yoruban individual, to experimentally validated genomic features. We found that de novo assemblies were 16.2% shorter than the reference genome and that 420.2 megabase pairs of common repeats and 99.1% of validated duplicated sequences were missing from the genome. Consequently, over 2,377 coding exons were completely missing. We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.8
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available