Virus identification software tools | Small RNA sequencing data analysis
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.
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. VirusDetect is available online upon registration or can be downloaded as a local standalone program.
Separates visualization from alignment. viRome is an R package that analyses short-read next-generation sequencing (NGS) data from virus-infection studies where the siRNA or piRNA pathways have been implicated. It produces a variety of plots and reports that are essential to the analysis of data from viral siRNA datasets. This package provides a range of functions to help scientists to visualize the results of such experiments.
A mapping package with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA presents the data graphically and shows statistical analyses directly from the large and complex sets of small RNA sequences from infected hosts, fitting together tools that were previously available only as independent scripts or softwares. SearchSmallRNA program is able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it is a valuable tool for viruses sequencing and discovery.