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.

Comments

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

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.

Language

en

File Format

application/pdf

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