Abstract
High-throughput sequencing emerged as a powerful approach to characterize siRNA populations generated by hosts in response to viral infections. Here we described an informatic pipeline visitor to analyze in-house large sequencing datasets generated from Illumina sequencing of Drosophila small RNA libraries. The visitor perl script is designed to treat fastq sequence datasets from the Illumina sequencing platform, using a computer running under a UNIX compliant operating system (MacOS X, Linux, etc.). visitor first generates a detailed report of the sequence quality of the Illumina run. Then, using the Novoalign software, the script removes reads that match with the D. melanogaster genome from the sequencing data set. The remaining reads are aligned to a viral reference library, which can contain one or several virus genomes. visitor provides a hit table of identified viral siRNAs as well as graphics eps files of viral siRNA profiles. Unmatched small RNAs are also available in a fast format for de novo assembly and new virus discovery.
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References
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Acknowledgments
The author would like to thank A.L Bougé, M.C. Saleh, and N. Vodovar for helpful discussions, testing, and encouragement and Marius van den Beek for beta-testing visitor. This work was supported by the Institut Pasteur, the Centre National de la Recherche Scientifique and funding from the Agence Nationale pour la Recherche (AKROSS program). The visitor script can be downloaded at http://drosophile.org/GEDlab/?page_id=254.
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© 2011 Humana Press
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Antoniewski, C. (2011). Visitor, An Informatic Pipeline for Analysis of Viral siRNA Sequencing Datasets. In: van Rij, R. (eds) Antiviral RNAi. Methods in Molecular Biology, vol 721. Humana Press. https://doi.org/10.1007/978-1-61779-037-9_7
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DOI: https://doi.org/10.1007/978-1-61779-037-9_7
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