Journal: Bioinformatics

Article Title: EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

doi: 10.1093/bioinformatics/btac176

Figure Lengend Snippet: SNVs, insertions and deletions that are shared, or specific to the EC-19 and Galaxy workflows

Article Snippet: To address this need, we developed EDGE COVID-19 (EC-19), a user-friendly, web-based platform that enables rapid and automated processing of FASTQ read datasets from either Illumina or Oxford Nanopore Technology (ONT) platforms generated using either amplicon or random shotgun-based methods.

Techniques:

Journal: Bioinformatics

Article Title: EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

doi: 10.1093/bioinformatics/btac176

Figure Lengend Snippet: Distribution of all SNV mutations detected by the EC-19 and Galaxy workflows, displaying depth of coverage (DP) ( X axis) and allele frequency (AF) ( Y axis). SNVs detected by both workflows for Illumina (left panel) and ONT (right panel) data are shown in gray (detected and called by both workflows) and black (detected by both but above 0.5 AF cutoff in only one workflow). SNV mutations detected by only one of the workflows yet not detected in the other are colored in red. A dotted vertical line is drawn at 100× Depth of coverage to separate SNVs with high and low depth of coverage. All the AFs and SNVs are based on EC-19 mapping, except for Galaxy specific SNVs

Article Snippet: To address this need, we developed EDGE COVID-19 (EC-19), a user-friendly, web-based platform that enables rapid and automated processing of FASTQ read datasets from either Illumina or Oxford Nanopore Technology (ONT) platforms generated using either amplicon or random shotgun-based methods.

Techniques: