Title |
VirusTAP: Viral Genome-Targeted Assembly Pipeline
|
---|---|
Published in |
Frontiers in Microbiology, February 2016
|
DOI | 10.3389/fmicb.2016.00032 |
Pubmed ID | |
Authors |
Akifumi Yamashita, Tsuyoshi Sekizuka, Makoto Kuroda |
Abstract |
Although next-generation sequencing (NGS) technology provides a comprehensive means with which to identify potential pathogens from clinical specimens, simple and user-friendly bioinformatics pipelines are expected to obtain the entire viral genome sequence, subsequently providing traceability, based on extensive molecular phylogenetic analyses. We have developed a web-based integrated NGS analysis tool for the viral genome (virus genome-targeted assembly pipeline: VirusTAP), which includes extensive sequence subtraction of host- or bacteria-related NGS reads prior to de novo assembly, leading to the prompt and accurate assembly of viral genome sequences from metagenomic NGS reads. The VirusTAP web site is at https://gph.niid.go.jp/cgi-bin/virustap/index.cgi/. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 30% |
Japan | 2 | 20% |
France | 1 | 10% |
Unknown | 4 | 40% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 7 | 70% |
Scientists | 3 | 30% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Brazil | 2 | 2% |
Switzerland | 1 | <1% |
South Africa | 1 | <1% |
Peru | 1 | <1% |
Spain | 1 | <1% |
Unknown | 110 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 33 | 28% |
Student > Ph. D. Student | 25 | 22% |
Student > Master | 18 | 16% |
Student > Bachelor | 7 | 6% |
Other | 5 | 4% |
Other | 11 | 9% |
Unknown | 17 | 15% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 46 | 40% |
Biochemistry, Genetics and Molecular Biology | 23 | 20% |
Immunology and Microbiology | 9 | 8% |
Medicine and Dentistry | 4 | 3% |
Environmental Science | 4 | 3% |
Other | 11 | 9% |
Unknown | 19 | 16% |