No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Abstract

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2. The initial publications describing genomic features of SARS-CoV-2 [1-4] used Illumina and Oxford nanopore data to elucidate the sequence composition of patient specimens (although only Wu and colleagues [3] explicitly provided the accession numbers for their raw short-read sequencing data). However, their approaches to processing, assembly, and analysis of raw data differed widely (Table 1) and ranged from transparent [3] to entirely opaque [4]. Such lack of analytical transparency sets a dangerous precedent. Infectious disease outbreaks often occur in

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

“…Through these components, thousands of genomics analysis tools and workflows are available for a wide variety of analyses. This includes population-scale variant calling with GATK or freebayes (Garrison & Marth, 2012; Van der Auwera et al, 2013), gene expression analysis for both bulk and single cell datasets (Amezquita et al, 2020; Grabherr et al, 2011; Li et al, 2020), methylation analysis (Krueger & Andrews, 2011), COVID-19 viral genomics analysis workflows (Baker et al, 2020; Lemieux et al, 2021), and thousands more. For example, Supplemental Note 1 displays the workspace for germline variant calling using GATK4.…”

HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations

“…Additionally, our commitment to ensuring the public availability of best practices for genomics workflows is carried out through our choice of Bioconda for installing HAPHPIPE. HAPHPIPE provides a user-friendly framework for operating many community-supported open source tools, the underutilization of which, and the resulting implications for rigor and reproducibility in viral genomics, have been brought to light by scientific response to the recent COVID-19 pandemic ( Baker et al 2020 ). It is our hope that our efforts will further support use, maintenance, and availability of open-source tools within the bioinformatics community.…”

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

“…[ 112 ]), analysis (e.g. [ 113 ]), and for the effective coordination of national scientific infrastructures (e.g. [ 46 ]).…”

“…COV3D [ 134 ] is a centralized resource for spike and other coronavirus protein structures, which provides effective and yet simple tools for the visualization of protein structures, along with the annotation of relevant functional elements or genomic variants. The Galaxy Europe server [ 135 ] incorporates a highly curated collection of tools and expert-made workflows for the analysis of COVID-19 data, along with pointers to many relevant datasets.…”