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 language | English (US) |
|---|---|
| Article number | 3 |
| Journal | Genome biology |
| Volume | 16 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 13 2015 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
- Cell Biology
Cite this
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 journal › Article
}
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 -