ALLMAPS: robust scaffold ordering based on multiple maps

Date
2015-01-13
Authors
Tang, Haibao
Zhang, Xingtan
Miao, Chenyong
Zhang, Jisen
Ming, Ray
Schnable, James
Schnable, Patrick
Lyons, Eric
Lu, Jianguo
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Agronomy
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AgronomyAgronomy
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.

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This article is from Genome Biology 16 (2015): 3, doi:10.1186/s13059-014-0573-1. Posted with permission.

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