Run Module - serratus-bio/open-virome GitHub Wiki

The SRA Run module encapsulates mandatory metadata fields associated with the SRA Run and BioProject. Optional metadata included with SRA BioSamples are presented in other modules.

Plots include a Target set and Control set. The Target set includes samples that match the user's query AND contain viruses. The Control set are any samples that are in BioProjects matching the user's query but are not in the Target set.

Run Label

This is the "organism" label provided by the submitter. Although it is listed as organism, it can include any label that maps to a tax_id in the NCBI Taxonomy. Since it's assigned by users and not validated, it's generally not reliable. Using sOTU Palmprints or STAT organisms will be more reliable whenever possible.

Plots can display run count (number of samples), Giga base pairs, or percentage of total within the Target or Control set. The bar plots can be scrolled if >10 rows exist and the section is in 'Advanced' view.

Run Technology

This is the assay type used for sequencing provided by the submitter.

Plots can display run count (number of samples), Giga base pairs, or percentage of total within the Target or Control set.

BioProject

This is the SRA Bioproject which contains a set of Runs related to a given research project.

The plots show the distribution of sizes of BioProjects that match the user's query as well as distribution of the percentage of runs within each BioProject that match the target set (coverage).