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Limitations of next-generation genome sequence assembly
Eichler, Evan E ; Alkan, Can ; Sajjadian, Saba
Nature methods, 2011-01, Vol.8 (1), p.61-65
[Periódico revisado por pares]
United States: Nature Publishing Group
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Título:
Limitations of next-generation genome sequence assembly
Autor:
Eichler, Evan E
;
Alkan, Can
;
Sajjadian, Saba
Assuntos:
Algorithms
;
Base Sequence
;
Biotechnology
;
Comparative studies
;
DNA sequencing
;
Evolution, Molecular
;
Experiments
;
Genome, Human - genetics
;
Genomics
;
Genomics - economics
;
Genomics - methods
;
Genomics - trends
;
Humans
;
Methods
;
Nucleotide sequencing
;
Research methodology
;
Sequence Analysis, DNA - economics
;
Sequence Analysis, DNA - methods
;
Sequence Analysis, DNA - standards
;
Sequence Analysis, DNA - trends
É parte de:
Nature methods, 2011-01, Vol.8 (1), p.61-65
Notas:
ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ObjectType-Article-1
ObjectType-Feature-2
AUTHOR CONTRIBUTIONS
C.A. and E.E.E. conceived the study and wrote the manuscript. C.A. and S.S. analyzed the data.
Descrição:
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.
Editor:
United States: Nature Publishing Group
Idioma:
Inglês
Links
View this record in MEDLINE/PubMed
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