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All Projects → yyoshiaki → VIRTUS

yyoshiaki / VIRTUS

Licence: other
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Programming Languages

Common Workflow Language
39 projects
python
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Labels

rnaseqcwlvirus-detection

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VIRTUS : VIRal Transcript Usage Sensor v1.2.1

!! VIRTUS2 is now available in https://github.com/yyoshiaki/VIRTUS2

Virus transcript detection and quantification using normal human RNAseq. VIRTUS is the first tool to detect viral transcripts considering their splicing event rather than the viral genome copy number. VIRTUS can be applied to both bulk RNAseq and single-cell RNAseq. The virus reference covers 762 viruses including SARS-CoV-2 (cause of COVID-19). The workflow is implemented by Common Workflow Language and Rabix. You can specify each parameter individually or give yaml or json file which describes all the parameter information. In detail, check the CWL User Guide out.

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Documentation

First, refer to WIKI. We recommend walking through Quick tutorial.

Contact

Yoshiaki Yasumizu ([email protected])

Citation

VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data Yasumizu, Yoshiaki, Atsushi Hara, Shimon Sakaguchi, and Naganari Ohkura. 2020. “OUP Accepted Manuscript.” Edited by Jan Gorodkin. Bioinformatics, October. https://doi.org/10.1093/bioinformatics/btaa859.

Acknowledgement

  • Kozo Nishida : CI config and many other supports.
  • Ayano Onishi : Logo design.

Licence

This software is freely available for academic users. Usage for commercial purposes is not allowed. Please refer to the LICENCE page.

Creative Commons License

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