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ALLMAPS: robust scaffold ordering based on multiple maps.

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 .

SUBMITTER: Tang H

PROVIDER: S-EPMC4305236 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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ALLMAPS: robust scaffold ordering based on multiple maps.

Tang Haibao H Zhang Xingtan X Miao Chenyong C Zhang Jisen J Ming Ray R Schnable James C JC Schnable Patrick S PS Lyons Eric E Lu Jianguo J

Genome biology 20150113

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 mappi ...[more]

PMID: 25583564

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