The JGI Analysis Workflow Service (JAWS) is a scalable and centralized workflow execution framework developed by the U.S. Department of Energy Joint Genome Institute (JGI, jgi.doe.gov). It enables researchers to efficiently run complex computational workflows across multiple high-performance computing (HPC) resources. JAWS automates resource configuration, data transfer, and job scheduling, allowing users to focus on their scientific tasks while ensuring workflow reproducibility and scalability.JAWS takes advantage of robust software packages, Docker containers, and the Workflow Description Language (WDL) as building blocks for standardized, Findable, Accessible, Interoperable, Reusable (FAIR) workflows. Over the past five years, we have collaborated with users at the JGI and the National Microbiome Data Collaborative (NMDC) to execute their pipelines on resources at the National Energy Research Scientific Computing Facility (NERSC), Pacific Northwest National Laboratory (PNNL), and on JGI-owned resources at Lawrence Berkeley National Laboratory (LBNL). The model of having a workflow protocol (WDL), software environment (Docker container), and input data has worked incredibly well for users. JAWS has been able to scale to support thousands of jobs, and the effort to standardize the workflows has yielded significant performance improvements. The software is open-source and available under the BSSD license.

SUMMARY: Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. AVAILABILITY AND IMPLEMENTATION: https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. AVAILABILITY AND IMPLEMENTATION: The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.