GEMS Study of Diarrheal Disease

This page contains data related to the GEMS study of diarrheal disease in children under 5 years of age from low-income countries.


Metagenomic datasets prove challenging to assemble using traditional assembly pipelines designed for individual genomes. Using AMOS as a foundation, we have created a robust & easy-to-use metagenomic assembly pipeline that takes reads (FASTA,FASTQ,SFF) and assembles them into Unitigs (CABOG,NEWBLER,Minimus,SOAPdenovo), Contigs & Scaffolds (Bambus2) & ORFs (Glimmer MG, MetaGeneMark), and annotates results using Metaphyler and a graph-based propagation method.


MetaPath can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge.


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