ALLMAPS: Robust scaffold ordering based on multiple maps

Haibao Tang, Xingtan Zhang, Chenyong Miao, Jisen Zhang, Ray Ming, James C. Schnable, Patrick S. Schnable, Eric Lyons, Jianguo Lu

Research output: Contribution to journalArticle

Abstract

The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.

Original languageEnglish (US)
Article number3
JournalGenome biology
Volume16
Issue number1
DOIs
StatePublished - Jan 13 2015
Externally publishedYes

Fingerprint

genome assembly
Genome
genome
Chromosomes
chromosomes
genomics
chromosome
methodology

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Tang, H., Zhang, X., Miao, C., Zhang, J., Ming, R., Schnable, J. C., ... Lu, J. (2015). ALLMAPS: Robust scaffold ordering based on multiple maps. Genome biology, 16(1), [3]. https://doi.org/10.1186/s13059-014-0573-1

ALLMAPS : Robust scaffold ordering based on multiple maps. / Tang, Haibao; Zhang, Xingtan; Miao, Chenyong; Zhang, Jisen; Ming, Ray; Schnable, James C.; Schnable, Patrick S.; Lyons, Eric; Lu, Jianguo.

In: Genome biology, Vol. 16, No. 1, 3, 13.01.2015.

Research output: Contribution to journalArticle

Tang, H, Zhang, X, Miao, C, Zhang, J, Ming, R, Schnable, JC, Schnable, PS, Lyons, E & Lu, J 2015, 'ALLMAPS: Robust scaffold ordering based on multiple maps', Genome biology, vol. 16, no. 1, 3. https://doi.org/10.1186/s13059-014-0573-1
Tang, Haibao ; Zhang, Xingtan ; Miao, Chenyong ; Zhang, Jisen ; Ming, Ray ; Schnable, James C. ; Schnable, Patrick S. ; Lyons, Eric ; Lu, Jianguo. / ALLMAPS : Robust scaffold ordering based on multiple maps. In: Genome biology. 2015 ; Vol. 16, No. 1.
@article{7d06002896ea414387f1ccd0b15696b6,
title = "ALLMAPS: Robust scaffold ordering based on multiple maps",
abstract = "The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.",
author = "Haibao Tang and Xingtan Zhang and Chenyong Miao and Jisen Zhang and Ray Ming and Schnable, {James C.} and Schnable, {Patrick S.} and Eric Lyons and Jianguo Lu",
year = "2015",
month = "1",
day = "13",
doi = "10.1186/s13059-014-0573-1",
language = "English (US)",
volume = "16",
journal = "Genome Biology",
issn = "1465-6906",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - ALLMAPS

T2 - Robust scaffold ordering based on multiple maps

AU - Tang, Haibao

AU - Zhang, Xingtan

AU - Miao, Chenyong

AU - Zhang, Jisen

AU - Ming, Ray

AU - Schnable, James C.

AU - Schnable, Patrick S.

AU - Lyons, Eric

AU - Lu, Jianguo

PY - 2015/1/13

Y1 - 2015/1/13

N2 - The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.

AB - The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.

UR - http://www.scopus.com/inward/record.url?scp=84939170283&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84939170283&partnerID=8YFLogxK

U2 - 10.1186/s13059-014-0573-1

DO - 10.1186/s13059-014-0573-1

M3 - Article

C2 - 25583564

AN - SCOPUS:84939170283

VL - 16

JO - Genome Biology

JF - Genome Biology

SN - 1465-6906

IS - 1

M1 - 3

ER -