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Genome Biol. 2015 Jan 13;16:3. doi: 10.1186/s13059-014-0573-1.

ALLMAPS: robust scaffold ordering based on multiple maps.

Author information

1
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. tanghaibao@gmail.com.
2
School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA. tanghaibao@gmail.com.
3
Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. tanghaibao@gmail.com.
4
J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD, 20850, USA. tanger.zhang@gmail.com.
5
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. miaochenyong@163.com.
6
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. zjisen@gmail.com.
7
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. rming@life.illinois.edu.
8
Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. james.schnable@gmail.com.
9
Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA. james.schnable@gmail.com.
10
Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. schnable@iastate.edu.
11
Department of Agronomy, Iowa State University, Ames, IA, 50011, USA. schnable@iastate.edu.
12
School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA. elyons.uoa@gmail.com.
13
Heilongjiang River Fisheries Research Institute, Harbin, 150070, China. jianguonk@gmail.com.

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 .

PMID:
25583564
PMCID:
PMC4305236
DOI:
10.1186/s13059-014-0573-1
[Indexed for MEDLINE]
Free PMC Article

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