BAGS-Shiny

Launch App Logo

Application

Name
BAGS-Shiny
Type
ShinyProxy App
URL
https://bags.serve.scilifelab.se
Source Code
https://github.com/lfdelzam/Gene_Catalog_Rshiny
Image
ghcr.io/alfredeen/gene_catalog_rshiny:main-20250702-1117
Created
11 Apr, 2025
Updated
02 Jul, 2025
Tags
bags

Biome-specific gene catalogues have been recovered for many environments using shotgun metagenomics, followed by assembly and gene calling on the assembled contigs. We recently proposed a novel mix-assembly strategy, combining individual and co-assembly approaches, and used this approach to assemble an extensive non-redundant gene set from 124 Baltic Sea metagenome samples. The Baltic Sea Gene Set (BAGS v1.1) comprises 66.53 million functionally and taxonomically annotated genes. To enable interactive exploration of this gene catalogue we have developed an RShiny application, BAGS-Shiny, that allows users to perform searches by sequence similarity (BLAST) and/or taxonomic and functional annotation. The gene catalogue and web application will serve as valuable tools for exploring microbial gene functions in brackish ecosystems.

Software

Type
Cloud Application
Operating System
Kubernetes
Version
ghcr.io/scilifelabdatacentre/serve-charts/shinyproxy:1.4.5

Resource

CPU Request
100m
CPU Limit
12
Memory Request
1Gi
Memory Limit
48Gi
Storage Request
200Mi
Storage Limit
5000Mi

Project

Name
BAGS-Shiny
Created
25 Mar, 2024

A web-based interactive tool for exploring the Baltic Sea microbial gene set.

Owner
Anders Andersson
anders.andersson@scilifelab.se
Gene Technology
other