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 journalArticlepeer-review

241 Scopus citations


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:

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

ASJC Scopus subject areas

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


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