Title |
Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences
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Published in |
Giga Science, August 2016
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DOI | 10.1186/s13742-016-0141-6 |
Pubmed ID | |
Authors |
Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli, Stephen J. O’Brien |
Abstract |
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. 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. 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. |
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United States | 5 | 31% |
France | 2 | 13% |
Sweden | 1 | 6% |
United Kingdom | 1 | 6% |
Netherlands | 1 | 6% |
India | 1 | 6% |
Hong Kong | 1 | 6% |
Unknown | 4 | 25% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 8 | 50% |
Scientists | 7 | 44% |
Science communicators (journalists, bloggers, editors) | 1 | 6% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 1 | <1% |
Hungary | 1 | <1% |
Netherlands | 1 | <1% |
Unknown | 155 | 98% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 40 | 25% |
Researcher | 32 | 20% |
Student > Bachelor | 21 | 13% |
Student > Master | 15 | 9% |
Student > Doctoral Student | 7 | 4% |
Other | 22 | 14% |
Unknown | 21 | 13% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 62 | 39% |
Biochemistry, Genetics and Molecular Biology | 51 | 32% |
Computer Science | 7 | 4% |
Veterinary Science and Veterinary Medicine | 2 | 1% |
Unspecified | 2 | 1% |
Other | 10 | 6% |
Unknown | 24 | 15% |