WGSA2 – An assembly-based shotgun metagenomics data analysis pipeline, implemented online in Nephele, a microbiome analysis cloud platform

Authors

• AG Angela
• D Doan
• P Subramanian
• M Quinones
• L Kim
• M Dolan

Abstract

Widespread interest in microbiome exploration has resulted in the development of various powerful computational tools and pipelines online, which can save the researcher from the burden of bioinformatics processing of their metagenomics data. Among these, some can extract taxonomic and functional information directly from shotgun metagenomic short reads (e.g. MetaPhlAn). However, more comprehensive analysis require longer contiguous sequences (e.g. KEGG tools, BLASTp). Unfortunately, there is a scarcity of online tools that provide researchers with computational resources and a command line-free experience to assemble short-read metagenomic datasets for deeper exploration. To bridge this computational gap, we have designed, developed, and integrated a command line-free Whole Metagenome Sequencing Assembly-based pipeline – WGSA2, into our cloud-based microbiome analysis platform, Nephele (https://nephele.niaid.nih.gov/).

The WGSA2 pipeline processes shotgun datasets from complex microbial communities and diverse habitats (both host-associated and environmental) producing visualizations and summarized output based on functional and taxonomic annotation and binning of assemblies. The pipeline provides a user-friendly experience, that omits computational demands and experience, allows for processing customizations including a choice of databases (e.g. RefSeq, MGBC, KEGG, MetaCyc) and for efficient acquisition of biological detail. Overall, the WGSA2 pipeline allows users to gain an understanding of their metagenomic dataset as well as easy access to an assembly-based sequence and analysis of their dataset.

Scientific Focus Area: Computational Biology

This page was last updated on Monday, September 25, 2023