Challenges in the analysis of viral metagenomes

Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia

The characterization of unknown viral entities in the environment is now possible with modern sequencing; however, current tooling for exploiting these data represents a practical and methodological bottleneck for effective data analysis. Practically, most available software tools are inaccessible to the majority of potential users, demanding expertise and computing resources often lacked by the researchers from diverse backgrounds involved in sample collection, sequencing, and analysis. There is a need for robust and intuitive analytical tools without requirements for fast internet connectivity, which may be unavailable in remote or developing regions. More fundamentally, the intended scope of published analytical tools and workflows is often less than clear, and given the diverse applications of viral sequencing, it can be difficult to gauge the relevance of newly published tools without first testing them. For example, a fast sequence classifier might fail entirely to detect a novel strain of a well-characterized virus, and equally might perform well with Illumina sequences yet deliver poor results for data generated with the Ion Torrent platform. Furthermore, results arising from these analyses should be replicable, intelligible, and useful to the end user, with provision for quality control and error management. Software tools that target expert users should be tested, documented and robustly distributed as packages or containers so as to streamline the processes of installation and generating results.