Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Abstract

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.

Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples

“…Quality control, de novo assembly, taxonomic classification, and reference-based analyses were conducted using EDGE Bioinformatic software v 2.0 [27] with default parameters and host removal of human reference GRCh38 and also with CLC Genomics Workbench v11 (QIAGEN Bioinformatics; Redwood City, CA). The reference mapping parameters in CLC were modified from defalt settings to 0.8 length fraction and 0.8 similarity fraction with global alignment and random mapping of non-specific matches.…”

Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota

“…Preprocessing of the HiSeq data using the EDGE pipeline (20) discarded 0.15-0.22% reads and trimmed 0.31-0.41% of bases by the initial quality control. It then removed 0.20-0.93% of the filtered reads that were mapped to the human genome, which was unexpectedly small; this was likely because of our protocol using a saliva DNA collection kit for microbes and viruses followed by the enzymatic DNA extraction.…”

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

“…Even so, the capabilities of Sunbeam compare favorably with existing pipelines such as SURPI (Sequencebased Ultra-Rapid Pathogen Identification) [17], EDGE (Empowering the Development of Genomics Expertise) [29], ATLAS (Automatic Tool for Local Assembly Structures) [30], and KneadData [31], (Table S1). Where Sunbeam's primary advancements lie are in its ease of deployment, extension framework, and novel algorithmic solutions to the issues of low-complexity or host-derived sequence filtering.…”

“…To make the framework widely useful, users must be able to straightforwardly add new steps into the workflow as needed and share them with others. Several pipelines have been developed that achieve many of these goals [17,[29][30][31], but did not meet our needs for greater flexibility in processing metagenomic datasets and long-term reproducibility of analyses.…”