Agronomy and Horticulture Department


Date of this Version



Tang et al. Genome Biology (2015) 16:3 DOI 10.1186/s13059-014-0573-1


© 2015 Tang et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. Used by permission.


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: