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 .
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. tanghaibao@gmail.com.|School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA. tanghaibao@gmail.com.|Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. tanghaibao@gmail.com.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD, 20850, USA. tanger.zhang@gmail.com.
authors.forename: Xingtan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. miaochenyong@163.com.
authors.forename: Chenyong
authors.initials: C
authors.lastname: Miao
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. zjisen@gmail.com.
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. rming@life.illinois.edu.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
authors.affiliation: Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. james.schnable@gmail.com.|Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA. james.schnable@gmail.com.
authors.forename: James C
authors.initials: JC
authors.lastname: Schnable
authors.affiliation: Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. schnable@iastate.edu.|Department of Agronomy, Iowa State University, Ames, IA, 50011, USA. schnable@iastate.edu.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
authors.affiliation: School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA. elyons.uoa@gmail.com.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: Heilongjiang River Fisheries Research Institute, Harbin, 150070, China. jianguonk@gmail.com.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D000818:Animals; D002397:Catfishes / Q000235:genetics; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D016000:Cluster Analysis; D003198:Computer Simulation; D030541:Databases, Genetic; D008040:Genetic Linkage; D005819:Genetic Markers; D016678:Genome; D023281:Genomics / Q000379:methods*; D029902:Medicago / Q000235:genetics; D012984:Software
chemical_list: D005819:Genetic Markers