Campus Units
Plant Biology, Agronomy
Document Type
Article
Publication Version
Published Version
Publication Date
1-13-2015
Journal or Book Title
Genome Biology
Volume
16
First Page
3
DOI
10.1186/s13059-014-0573-1
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.
Rights
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Copyright Owner
Tang et al.
Copyright Date
2015
Language
en
File Format
application/pdf
Recommended Citation
Tang, Haibao; Zhang, Xingtan; Miao, Chenyong; Zhang, Jisen; Ming, Ray; Schnable, James C.; Schnable, Patrick S.; Lyons, Eric; and Lu, Jianguo, "ALLMAPS: robust scaffold ordering based on multiple maps" (2015). Agronomy Publications. 91.
https://lib.dr.iastate.edu/agron_pubs/91
Included in
Agricultural Science Commons, Agriculture Commons, Agronomy and Crop Sciences Commons, Genomics Commons, Plant Biology Commons, Plant Breeding and Genetics Commons
Comments
This article is from Genome Biology 16 (2015): 3, doi:10.1186/s13059-014-0573-1. Posted with permission.