Title |
Genomer — A Swiss Army Knife for Genome Scaffolding
|
---|---|
Published in |
PLOS ONE, June 2013
|
DOI | 10.1371/journal.pone.0066922 |
Pubmed ID | |
Authors |
Michael D. Barton, Hazel A. Barton |
Abstract |
The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe "Genomer," a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 8 | 31% |
Canada | 3 | 12% |
Germany | 2 | 8% |
United Kingdom | 2 | 8% |
France | 1 | 4% |
Norway | 1 | 4% |
Bosnia and Herzegovina | 1 | 4% |
Cameroon | 1 | 4% |
Unknown | 7 | 27% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 15 | 58% |
Members of the public | 10 | 38% |
Practitioners (doctors, other healthcare professionals) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 9% |
Netherlands | 1 | 3% |
Brazil | 1 | 3% |
Canada | 1 | 3% |
Sweden | 1 | 3% |
Japan | 1 | 3% |
Spain | 1 | 3% |
Unknown | 25 | 74% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 13 | 38% |
Student > Bachelor | 4 | 12% |
Professor | 4 | 12% |
Student > Postgraduate | 4 | 12% |
Professor > Associate Professor | 3 | 9% |
Other | 5 | 15% |
Unknown | 1 | 3% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 24 | 71% |
Computer Science | 3 | 9% |
Biochemistry, Genetics and Molecular Biology | 2 | 6% |
Engineering | 2 | 6% |
Environmental Science | 1 | 3% |
Other | 0 | 0% |
Unknown | 2 | 6% |