Biology Faculty Articles
Title
Chromosomer: A Reference-Based Genome Arrangement Tool for Producing Draft Chromosome Sequences
Document Type
Article
Publication Date
8-22-2016
Publication Title
GigaScience
Keywords
Reference-assisted assembly, Chromosome assembly, Alignment
ISSN
2047-217X
Volume
5
Issue/No.
38
First Page
1
Last Page
11
Abstract
Background: As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes.
Findings: We developed Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process.
Conclusions: Despite implementing a straightforward alignment-based approach, Chromosomer is a useful tool for genomic analysis of species without chromosome maps. Putative chromosome assemblies by Chromosomer can be used in comparative genomic analysis, genomic variation assessment, potential linkage group inference and other kinds of analysis involving contig or scaffold mapping to a high-quality assembly.
Additional Comments
Russian Ministry of Science mega-grant #11.G34.31.0068
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
NSUWorks Citation
Tamazian, Gaik; Pavel Dobrynin; Ksenia Krasheninnikova; Aleksey Komissarov; Klaus-Peter Koepfli; and Stephen J. O'Brien. 2016. "Chromosomer: A Reference-Based Genome Arrangement Tool for Producing Draft Chromosome Sequences." GigaScience 5, (38): 1-11. doi:10.1186/s13742-016-0141-6.
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
DOI
10.1186/s13742-016-0141-6
Comments
© 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.