Omerza, G. | Search bioRxiv

bioRxiv2022

saks-nf: A json solution for Nextflow pipeline construction

To address the increasing complexity of data in scientific research, researchers have developed many workflow manager tools. Nextflow is one of the most widely used tools, enabling scalability and reproducibility of scientific workflows across various computational platforms through the implementation of domain-specific language (DSL) with a dataflow paradigm. We developed saks-nf, a JavaScript Object Notation (JSON) solution for constructing Nextflow pipelines. Our solution flattens the learning curve for Nextflow. Users can build and maintain a pipeline without prior programming experience by editing a JSON specification on any text editor. The saks-nf solution can be used to construct a multi-step pipeline with parallel and scatter-gather capacity in a computing platform of choice, such as a local machine, a high-performance cluster, or cloud computing. This solution allows users to focus on analysis, thereby increasing productivity.

bioinformatics↗

bioRxiv2021

Subgenomic RNAs as molecular indicators of asymptomatic SARS-CoV-2 infection

In coronaviridae such as SARS-CoV-2, subgenomic RNAs (sgRNA) are replicative intermediates, therefore, their abundance and structures could infer viral replication activity and severity of host infection. Here, we systematically characterized the sgRNA expression and their structural variation in 81 clinical specimens collected from symptomatic and asymptomatic individuals with a goal of assessing viral genomic signatures of disease severity. We demonstrated the highly coordinated and consistent expression of sgRNAs from individuals with robust infections that results in symptoms, and found their expression is significantly repressed in the asymptomatic infections, indicating that the ratio of sgRNAs to genomic RNA (sgRNA/gRNA) is highly correlated with the severity of the disease. Using long read sequencing technologies to characterize full-length sgRNA structures, we also observed widespread deletions in viral RNAs, and identified unique sets of deletions preferentially found primarily in symptomatic individuals, with many likely to confer changes in SARS-CoV-2 virulence and host responses. Furthermore, based on the sgRNA structures, the frequently occurred structural variants in SARS-CoV-2 genomes serves as a mechanism to further induce SARS-CoV-2 proteome complexity. Taken together, our results show that differential sgRNA expression and structural mutational burden both appear to be correlated with the clinical severity of SARS-CoV-2 infection. Longitudinally monitoring sgRNA expression and structural diversity could further guide treatment responses, testing strategies, and vaccine development.

microbiology↗