VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs
Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline t...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Elsevier
2017
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/80028 |
| _version_ | 1855539288578457600 |
|---|---|
| author | Yi Zheng Shan Gao Padmanabhan, C. Li, R. Galvez, M. Gutiérrez, D. Fuentes, S. Kai-Shu Ling Kreuze, Jan F. Zhangjun Fei |
| author_browse | Fuentes, S. Galvez, M. Gutiérrez, D. Kai-Shu Ling Kreuze, Jan F. Li, R. Padmanabhan, C. Shan Gao Yi Zheng Zhangjun Fei |
| author_facet | Yi Zheng Shan Gao Padmanabhan, C. Li, R. Galvez, M. Gutiérrez, D. Fuentes, S. Kai-Shu Ling Kreuze, Jan F. Zhangjun Fei |
| author_sort | Yi Zheng |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze largescale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. |
| format | Journal Article |
| id | CGSpace80028 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace800282024-11-15T08:53:04Z VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs Yi Zheng Shan Gao Padmanabhan, C. Li, R. Galvez, M. Gutiérrez, D. Fuentes, S. Kai-Shu Ling Kreuze, Jan F. Zhangjun Fei virus indexing rna rna sequence research Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze largescale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. 2017-01-01 2017-02-28T13:35:50Z 2017-02-28T13:35:50Z Journal Article https://hdl.handle.net/10568/80028 en Open Access Elsevier Zheng, Y.; Gaoa, S.; Padmanabhan, C.; Li, R.; Galvez, M.; Gutierrez, D.; Fuentes, S.; Ling, K.S.; Kreuze, J.; Fei, Z. 2017. VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology. (USA). ISSN 0042-6822. 500:130-138. |
| spellingShingle | virus indexing rna rna sequence research Yi Zheng Shan Gao Padmanabhan, C. Li, R. Galvez, M. Gutiérrez, D. Fuentes, S. Kai-Shu Ling Kreuze, Jan F. Zhangjun Fei VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs |
| title | VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs |
| title_full | VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs |
| title_fullStr | VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs |
| title_full_unstemmed | VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs |
| title_short | VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs |
| title_sort | virusdetect an automated pipeline for efficient virus discovery using deep sequencing of small rnas |
| topic | virus indexing rna rna sequence research |
| url | https://hdl.handle.net/10568/80028 |
| work_keys_str_mv | AT yizheng virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT shangao virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT padmanabhanc virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT lir virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT galvezm virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT gutierrezd virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT fuentess virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT kaishuling virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT kreuzejanf virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas AT zhangjunfei virusdetectanautomatedpipelineforefficientvirusdiscoveryusingdeepsequencingofsmallrnas |