Visitor, An Informatic pipeline for Analysis of Viral siRNA Sequencing Datasets

Published in:

“Antiviral RNAi” Methods in Molecular Biology™, 2011, Volume 721, Part 2, 123-142, DOI: 10.1007/978-1-61779-037-9_7

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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Manual available on request