Limitations of next-generation genome sequence assembly View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-11-21

AUTHORS

Can Alkan, Saba Sajjadian, Evan E Eichler

ABSTRACT

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. More... »

PAGES

61-65

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.1527

DOI

http://dx.doi.org/10.1038/nmeth.1527

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1015617800

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21102452


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