As sequencing costs drop, microbiome research is moving from 16S rRNA gene sequencing to
more comprehensive functional representations via whole genome or shotgun metagenomics
sequencing. Shotgun metagenomic sequencing is a relatively new environmental sequencing
approach used to examine thousands of organisms in parallel and comprehensively sample
all genes, providing insight into community biodiversity and function.
The following are the steps we follow to analyze metagenomics WGS samples:
Step 1 - Quality Control/Trimming
Step 2 - Run Assembly
De novo Assembly
Co-assembly
Reference-based Assembly
Step 3 - Quality Analysis of Assembled Contigs
Step 4 - Generate Contigs
Step 6 - Comparative Analysis
Choose best assembly for your data
Step 7a - Annotation on Assembled Contigs
Contigs selection
Gene calling
Taxonomic and functional annotation of genes
Step 7b - Coverage Binning
Back map contigs on their own reads to create .sam and .bam files using BBMAP
Find occurrence of uncultivated microbial populations
At USU’s high-performance computing and bioinformatics facility, we have developed a series of parallel, multicore, CPU-based,
open-source pipelines for large-scale -omics data analysis, which enables efficient and parallel analysis of multiple datasets
in a short period of time.
