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How metagenomics sequencing works

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
  • Bin Refinement
    • Clean up contamination
    • Select good quality bin
    • Bin taxonomic and functional classification