Title |
CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
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Published in |
BMC Bioinformatics, June 2014
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DOI | 10.1186/1471-2105-15-198 |
Pubmed ID | |
Authors |
Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain |
Abstract |
Detection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been developed to analyze NGS data but the resulting files are difficult to interpret without an additional visualization step. Circos (Genome Res, 19:1639-1645, 2009), a Perl script, is a powerful visualization software that requires setting up numerous configuration files with a large number of parameters to handle. R packages like RCircos (BMC Bioinformatics, 14:244, 2013) or ggbio (Genome Biol, 13:R77, 2012) provide functions to display genomic data as circular Circos-like plots. However, these tools are very general and lack the functions needed to filter, format and adjust specific input genomic data. |
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Geographical breakdown
Country | Count | As % |
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United States | 4 | 15% |
Japan | 3 | 12% |
Sweden | 2 | 8% |
France | 2 | 8% |
United Kingdom | 2 | 8% |
Canada | 1 | 4% |
India | 1 | 4% |
Brazil | 1 | 4% |
Germany | 1 | 4% |
Other | 1 | 4% |
Unknown | 8 | 31% |
Demographic breakdown
Type | Count | As % |
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Scientists | 18 | 69% |
Members of the public | 5 | 19% |
Science communicators (journalists, bloggers, editors) | 2 | 8% |
Practitioners (doctors, other healthcare professionals) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Norway | 2 | 2% |
United States | 2 | 2% |
France | 1 | <1% |
Australia | 1 | <1% |
United Kingdom | 1 | <1% |
Sweden | 1 | <1% |
Mexico | 1 | <1% |
Tunisia | 1 | <1% |
Unknown | 107 | 91% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 32 | 27% |
Student > Ph. D. Student | 27 | 23% |
Student > Master | 14 | 12% |
Student > Bachelor | 11 | 9% |
Professor > Associate Professor | 5 | 4% |
Other | 16 | 14% |
Unknown | 12 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 48 | 41% |
Biochemistry, Genetics and Molecular Biology | 24 | 21% |
Computer Science | 11 | 9% |
Medicine and Dentistry | 4 | 3% |
Environmental Science | 3 | 3% |
Other | 11 | 9% |
Unknown | 16 | 14% |