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

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108 Scopus citations

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

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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., Schnable, P. S., Lyons, E., & 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