Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences
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,...
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| Veröffentlicht in: | GigaScience 2016-08, Vol.5 (1), p.38-38, Article 38 |
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| creator | Tamazian, Gaik Dobrynin, Pavel Krasheninnikova, Ksenia Komissarov, Aleksey Koepfli, Klaus-Peter O'Brien, Stephen J |
| description | 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. |
| doi_str_mv | 10.1186/s13742-016-0141-6 |
| format | Article |
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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.
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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.</description><subject>Assemblies</subject><subject>Assembly</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes</subject><subject>Contig Mapping - methods</subject><subject>DNA sequencing</subject><subject>Gene mapping</subject><subject>Gene sequencing</subject><subject>Genome</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Inference</subject><subject>Linkage analysis</subject><subject>Methods</subject><subject>Nucleotide sequencing</subject><subject>Scaffolds</subject><subject>Sequence Alignment</subject><subject>Software</subject><subject>Technical Note</subject><issn>2047-217X</issn><issn>2047-217X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdUVGLFSEYlSjaZdsf0EsIvfQym47Op9NDsFxqN1jopaA3cfRzdpYZvelM0L_Py90uW4oofuccz-ch5DVnV5xreF-4ULJtGIe6JG_gGTlvmVRNy9WP50_OZ-SylAdWh1JaK_GSnLWqk71S7JyY3X1OSyppwfyBWpoxYMbosBlsQU9HjLVEbc42jrhgXOma0kxDynSfk9_cFEfqsw0rdScpWvDndlApr8iLYOeCl4_7Bfn--dO33W1z9_Xmy-76rnEdsLXxAbRjVmvwCoTvg7eDBrRBD4wNouuF63vvmMcWusHD0DHnwAsttehsYOKCfDzq7rdhQe-q0Wxns8_TYvNvk-xk_q3E6d6M6ZeRfS9bLavAu0eBnKr3spplKg7n2UZMWzFcc9Gz-tuqQt_-B31IW461PSO44NB2oHRFXR1Ro53RTDGk-q6r0-MyuRQxTPX-WgIHAAF9JfAjweVUSg3i5J4zc4jcHCM31YQ5RG6gct48bfvE-Buw-APy4Kkk</recordid><startdate>20160822</startdate><enddate>20160822</enddate><creator>Tamazian, Gaik</creator><creator>Dobrynin, Pavel</creator><creator>Krasheninnikova, Ksenia</creator><creator>Komissarov, Aleksey</creator><creator>Koepfli, Klaus-Peter</creator><creator>O'Brien, Stephen J</creator><general>Oxford University Press</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IAO</scope><scope>JQ2</scope><scope>K9.</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-2931-1123</orcidid></search><sort><creationdate>20160822</creationdate><title>Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences</title><author>Tamazian, Gaik ; 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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.</abstract><cop>United States</cop><pub>Oxford University Press</pub><pmid>27549770</pmid><doi>10.1186/s13742-016-0141-6</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-2931-1123</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Access via Oxford University Press (Open Access Collection); EZB-FREE-00999 freely available EZB journals; PubMed Central; Springer Nature OA/Free Journals |
| subjects | Assemblies Assembly Chromosome Mapping - methods Chromosomes Contig Mapping - methods DNA sequencing Gene mapping Gene sequencing Genome Genomes Genomic analysis Inference Linkage analysis Methods Nucleotide sequencing Scaffolds Sequence Alignment Software Technical Note |
| title | Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences |
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