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allmaps website  

The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. This process is often assisted by various mapping techniques. Because each map provides a unique line of evidence, a combination of multiple maps can greatly improve the accuracy of the resulting chromosomal assemblies. ALLMAPS is capable of computing a scaffold ordering that maximizes the colinearity to a collection of maps, including genetic, physical or comparative maps into the final chromosome build. We highlight several salient features of ALLMAPS.

Environment Modules

Run module spider allmaps to find out what environment modules are available for this application.

System Variables

  • HPC_ALLMAPS_DIR - installation directory
  • HPC_ALLMAPS_BIN - excutable directory


If you publish research that uses allmaps you have to cite it as follows:

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable J, Schnable P, Lyons E, Lu J. (2015) ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biology 16(1):3