Detection and correction of false segmental duplications caused by genome mis-assembly

David R. Kelley; Steven L. Salzberg

doi:10.1186/gb-2010-11-3-r28

Detection and correction of false segmental duplications caused by genome mis-assembly

David R. Kelley, Steven L. Salzberg

Research output: Contribution to journal › Article › peer-review

49 Scopus citations

Abstract

Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.

Original language	English (US)
Article number	r28
Journal	Genome biology
Volume	11
Issue number	3
DOIs	https://doi.org/10.1186/gb-2010-11-3-r28
State	Published - Mar 10 2010
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Access to Document

10.1186/gb-2010-11-3-r28

Cite this

@article{f3ea9076e60a4ca2918f95e8f7117d8c,

title = "Detection and correction of false segmental duplications caused by genome mis-assembly",

abstract = "Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.",

author = "Kelley, {David R.} and Salzberg, {Steven L.}",

note = "Funding Information: The authors thank Michael Schatz and Adam Phillippy for helpful discussion and comments on the manuscript. This work was supported in part by the National Institutes of Health under grants R01-LM006845 to SLS.",

year = "2010",

month = mar,

day = "10",

doi = "10.1186/gb-2010-11-3-r28",

language = "English (US)",

volume = "11",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central",

number = "3",

}

TY - JOUR

T1 - Detection and correction of false segmental duplications caused by genome mis-assembly

AU - Kelley, David R.

AU - Salzberg, Steven L.

N1 - Funding Information: The authors thank Michael Schatz and Adam Phillippy for helpful discussion and comments on the manuscript. This work was supported in part by the National Institutes of Health under grants R01-LM006845 to SLS.

PY - 2010/3/10

Y1 - 2010/3/10

N2 - Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.

AB - Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.

UR - http://www.scopus.com/inward/record.url?scp=77949428750&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77949428750&partnerID=8YFLogxK

U2 - 10.1186/gb-2010-11-3-r28

DO - 10.1186/gb-2010-11-3-r28

M3 - Article

C2 - 20219098

AN - SCOPUS:77949428750

SN - 1474-7596

VL - 11

JO - Genome biology

JF - Genome biology

IS - 3

M1 - r28

ER -

Detection and correction of false segmental duplications caused by genome mis-assembly

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this